Method of detecting cancer through generalized loss of stability of epigenetic domains, and compositions thereof

ABSTRACT

Provided herein is a method of detecting cancer through generalized loss of stability of epigenetic domains as well as compositions useful therein. The present invention is based on the discovery that generalized loss of stability of epigenetic domains was determined to be a characteristic across various cancer types. Genome-scale bisulfite sequencing of cancers revealed a surprising loss of methylation stability in the cancer methylome, involving both CpG islands and shores, as well as large (up to several megabases) blocks of hypomethylation affecting more than half of the genome, with concomitant stochastic variability in gene expression.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a 35 USC § 371 National Stage application of International Application No. PCT/US2012/037362 filed May 10, 2012; which claims the benefit under 35 USC § 119(e) to U.S. Application Ser. No. 61/518,892 filed May 12, 2011. The disclosure of each of the prior applications is considered part of and is incorporated by reference in the disclosure of this application.

GRANT INFORMATION

This invention was made with government support under Grant Nos. R37CA054358, R01HG005220, 5P50HG003233 and 5R01GM083084 awarded by the National Institutes of Health. The government has certain rights in the invention.

This invention was made with government support under grant numbers CA054358, HG005220, HG003233, and GM083084 awarded by the National Institutes of Health. The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

Field of the Invention

The present invention relates generally to methylome analysis, and more specifically to a method for detecting cancer through generalized loss of stability of epigenetic domains of the genome.

Background Information

Epigenetics is the study of non-sequence information of chromosome DNA during cell division and differentiation. The molecular basis of epigenetics is complex and involves modifications of the activation or inactivation of certain genes. Additionally, the chromatin proteins associated with DNA may be activated or silenced. Epigenetic changes are preserved when cells divide. Most epigenetic changes only occur within the course of one individual organism's lifetime, but some epigenetic changes are inherited from one generation to the next.

One example of an epigenetic mechanism is DNA methylation (DNAm), a covalent modification of the nucleotide cytosine. In particular, it involves the addition of methyl groups to cytosine nucleotides in the DNA, to convert cytosine to 5-methylcytosine. DNA methylation plays an important role in determining whether some genes are expressed or not. Abnormal DNA methylation is one of the mechanisms known to underlie the changes observed with aging and development of many cancers.

Cancers have historically been linked to genetic changes such as DNA sequence mutations. Evidence now supports that a relatively large number of cancers originate, not from mutations, but from epigenetic changes such as inappropriate DNA methylation. In some cases, hypermethylation of DNA results the an inhibition of expression of critical genes, such as tumor suppressor genes or DNA repair genes, allowing cancers to develop. In other cases, hypomethylation of genes modulates expression, which contributes to the development of cancer.

Cancer is generally viewed as over 200 separate organ-specific diseases of abnormal cell growth, largely controlled by a series of mutations, but also involving epigenetic, i.e. non-sequence based, changes that might involve the same sets of genes'. DNA methylation at CpG dinucleotides in particular has been studied extensively in cancer, with hypomethylation reported at some genes, hypermethylation at others, and a global loss of DNA methylation ascribed to repetitive DNA elements that are normally methylated.

Since the discovery of altered DNA methylation in human cancer, the focus of cancer epigenetics has been on candidate regions of the genome, either high-density CpG islands, gene promoters, or dispersed repetitive elements^(2,3), and there has not been a comprehensive genome-scale understanding of the relationship between DNA methylation loss and gain in cancer and in normal differentiation.

SUMMARY OF THE INVENTION

The present invention is based on the discovery that generalized loss of stability of epigenetic domains was determined to be characteristic across various cancer types. Genome-scale bisulfite sequencing of cancers revealed a surprising loss of methylation stability in the cancer methylome, involving both CpG islands and shores, as well as large (up to several megabases) blocks of hypomethylation affecting more than half of the genome, with concomitant stochastic variability in gene expression.

As such, in one aspect, a method of diagnosing cancer or a risk of cancer in a subject is provided. The method includes identifying an anti-profile in a sample from a subject including: i) determining the methylation status of a plurality of genomic nucleic acid sequences from a non-cancerous biological sample and corresponding plurality of genomic nucleic acid sequences in a test sample from the subject; ii) detecting a deviation in the methylation status from the test sample from the methylation status of the non-cancerous sample; iii) detecting an increased methylation variance in the test sample as compared to the non-cancerous sample; and iv) determining a methylation variance score by performing statistical analysis, thereby diagnosing cancer in the subject. In one embodiment, the method includes detecting the methylation status of one or more nucleic acid sequences selected from those set forth in Table 6, Table 7, Table 16 or Table 17. In one embodiment, the method further includes detecting expression of one or more genes as set forth in FIG. 16A, FIG. 16B, Table 3 or Table 5.

In another aspect, a method for providing a prognosis for cancer is provided. The method includes: a) comparing the methylation status of one or more nucleic acid sequences in a sample from a subject diagnosed with, or being treated for cancer, to a methylation status of the one or more nucleic acid sequences of a cancer cell; b) identifying a methylation anti-profile using the methylation status of (a) including: i) detecting a deviation in the methylation status of (a) from a methylation status of a corresponding plurality of nucleic acid sequences of a genome from a sample known to be non-cancerous; ii) detecting an increased methylation variance in the sample as compared to the non-cancerous sample; and iii) determining a methylation variance score by performing statistical analysis, wherein at least 25 nucleic acids are analyzed; and c) correlating the anti-profile of (b) with a prognosis, thereby providing a prognosis for cancer in the subject. In one embodiment the one or more nucleic acid sequences are selected from the group consisting of a nucleic acid sequence as set forth in Table 6, Table 7, Table 16 or Table 17, thereby providing a prognosis for the cancer. In one embodiment, the method further includes detecting expression of one or more genes as set forth in FIG. 16A, FIG. 16B, Table 3 or Table 5.

In another aspect, a method of diagnosing cancer in a subject is provided utilizing detection of a shift or loss of methylation boundary. The method includes: i) determining the methylation status of a plurality of genomic nucleic acid sequences from a non-cancerous biological sample and corresponding plurality of genomic nucleic acid sequences in a test sample from the subject; and ii) detecting a deviation in the methylation status from the test sample from the methylation status of the non-cancerous sample, wherein the deviation in the methylation status comprises a shift or loss of methylation boundary in one or more of the plurality of nucleic acid sequences in the test sample as compared to that of the corresponding plurality of nucleic acid sequences from the non-cancerous biological sample, thereby diagnosing cancer in the subject. In one embodiment, the plurality of nucleic acid sequences are selected from those set forth in Table 6, Table 7, Table 16 or Table 17. In various embodiment, a deviation is detected in at least about 10, 15, 25, 50, 100 or 1000 nucleic acids sequences.

In another aspect, a method for providing a prognosis for cancer in a subject utilizing detection of a shift or loss of methylation boundary. The method includes: a) detecting the methylation status of a plurality of nucleic acid sequences in a sample from a subject diagnosed with, or being treated for cancer; b) detecting a deviation in the methylation status from (a) as compared to a corresponding plurality of nucleic acid sequences of a genome from a sample known to be non-cancerous, wherein the deviation in the methylation status comprises a shift or loss of methylation boundary in the plurality of nucleic acid sequences in the sample from the subject diagnosed with, or being treated for cancer as compared to that of the corresponding plurality of nucleic acid sequences from the sample known to be non-cancerous; and c) correlating the deviation of (b) with a prognosis, thereby providing a prognosis for cancer in the subject. In one embodiment, the plurality of nucleic acid sequences are selected from those set forth in Table 6, Table 7, Table 16 or Table 17. In various embodiment, a deviation is detected in at least about 10, 15, 25, 50, 100 or 1000 nucleic acids sequences.

In another aspect, a method of diagnosing cancer in a subject is provided utilizing detection of hypomethylated genomic block regions. The method includes: i) determining the methylation status of a plurality of genomic nucleic acid sequences from a non-cancerous biological sample and corresponding plurality of genomic nucleic acid sequences in a test sample from the subject; and ii) detecting a deviation in the methylation status from the test sample from the methylation status of the non-cancerous sample, wherein the deviation in the methylation status comprises an increase in hypomethylation in the plurality of nucleic acid sequences in the test sample as compared to that of the corresponding plurality of nucleic acid sequences from the non-cancerous biological sample, and wherein the plurality of nucleic acid sequences is selected from those set forth in Table 6 [genomic block sequences], thereby diagnosing cancer in the subject. In various embodiment, a deviation is detected in at least about 10, 15, 25, 50, 100 or 1000 nucleic acids sequences.

In another aspect, a method for providing a prognosis for cancer in a subject utilizing detection of hypomethylated genomic block regions. The method includes: a) detecting the methylation status of a plurality of nucleic acid sequences in a sample from a subject diagnosed with, or being treated for cancer; b) detecting a deviation in the methylation status from (a) as compared to a corresponding plurality of nucleic acid sequences of a genome from a sample known to be non-cancerous, wherein the deviation in the methylation status comprises an increase in hypomethylation in the plurality of nucleic acid sequences in the sample from the subject as compared to that of the corresponding plurality of nucleic acid sequences from the sample known to be non-cancerous, and wherein the plurality of nucleic acid sequences is selected from those set forth in Table 6 [genomic block sequences]; and c) correlating the deviation of (b) with a prognosis, thereby providing a prognosis for cancer in the subject. In various embodiment, a deviation is detected in at least about 10, 15, 25, 50, 100 or 1000 nucleic acids sequences.

In another aspect, a plurality of nucleic acid sequences is provided. The nucleic acid sequences are capable of selectively hybridizing to a nucleic acid sequence selected from cancer-specific differentially methylated regions (cDMRs) as set forth in Table 17, wherein the cDMRs are stochastically methylated in cancer. In one embodiment, each nucleic acid sequence is about 10-55 base pairs in length.

In another aspect, a microarray is provided which includes the plurality of nucleic acid sequences as described herein.

In another aspect, a method of performing methylation analysis of genomic DNA isolated from a cell. The method includes performing comprehensive high-throughput array for relative methylation (CHARM) analysis on a sample of labeled, digested genomic DNA isolated from the cell using the microarray described herein, thereby performing methylation analysis.

In another aspect, a method of determining a therapeutic regimen for a subject is provided. The method includes a) analyzing a determined methylation profile; and b) determining an appropriate therapeutic regimen based on the analysis, thereby determining a therapeutic regime for the subject.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a graphical plot of number of reads and alignments obtained from bisulfite sequencing.

FIG. 2 is a graphical plot of estimated unmethylated cytosine conversion rate.

FIG. 3 is a graphical representation of bisulfite read position bias in evidence for methylation.

FIG. 4 is a graphical representation of methylation estimates obtained by high-frequency smoothing.

FIG. 5 is series of graphical representations of methylation patterns. FIG. 5(a) presents analysis of three normal samples (three top lines of center box) and matched cancers (three bottom lines of center box).

FIG. 6 is a series of graphical plots of methylation variance of common CpG sites across human cancer types. FIG. 6(a) plots methylation variance of common CpG sites in colon cancer. FIG. 6(b) plots methylation variance of common CpG sites in colon cancer. FIG. 6(b) plots methylation variance of common CpG sites in lung cancer. FIG. 6(c) plots methylation variance of common CpG sites in breast cancer. FIG. 6(d) plots methylation variance of common CpG sites in thyroid cancer. FIG. 6(e) plots methylation variance of common CpG sites in kidney (Wilms) cancer. FIG. 6(f) is a heatmap of the methylation values for CpGs clearly distinguishing the tissue types.

FIG. 7 is a series of graphical plots of methylation estimates plotted against genomic location for normal samples and cancer samples. The small DMR locations are shaded. Grey bars indicate the location of blocks, CpG islands, and gene exons. Tick marks along the bottom axis indicate the location of CpGs. FIG. 7(a) is a praphical plot of a methylation boundary shift outward (normal-top lines in shaded area; cancer-bottom lines in shaded area). FIG. 7(b) is a praphical plot of a methylation boundary shift inward (cancer-top lines in shaded area; normal-bottom lines in shaded area). FIG. 7(c) is a praphical plot of a loss of methylation boundary (cancer-top lines in shaded area normal-bottom lines in shaded area). FIG. 7(d) is a praphical plot of a novel hypomethylation DMR (normal-top lines in shaded area; cancer-bottom lines in shaded area).

FIG. 8 is a series of graphical plots of: (a) methylation differences; (b) copy number alterations; and (c) differences in methylation plotted against difference in copy number.

FIG. 9 is a series of clusters of methylation profiles using Euclidean distance. FIG. 9(a) is clustering of normal and colon tissues. FIG. 9(b) is clustering of normal and lung tissues. FIG. 9(c) is clustering of normal and breast tissues. FIG. 9(d) is clustering of normal and thyroid tissues. FIG. 9(e) is clustering of normal and kidney (Wilms) tissues.

FIG. 10 is a series of graphical representations. FIG. 10(a) is a plot of smoothed methylation values from bisulfite sequencing data for cancer samples and normal samples. FIG. 10(b) are smoothed methylation values from bisulfite sequencing data for cancer samples and normal samples. FIG. 10(c) is a plot of the distribution of methylation values for the normal samples versus the cancer samples. FIG. 10(d) is a plot of the distribution of methylation values in the blocks (solid lines) and outside the blocks (dashed lines) for normal samples and cancer samples. FIG. 10(e) is a plot of the distribution of methylation differences between cancer and normal samples stratified by inclusion in repetitive DNA and blocks.

FIG. 11 is a series of graphical plots of the distribution of methylation differences between cancer and normal samples stratified by repeat family and inclusion in blocks.

FIG. 12 is a series of graphical plots comparing CHARM microarray data and bisulfite sequencing for measuring methylation in (a) normal and (b) cancer samples.

FIG. 13 is a series of graphical plots. FIG. 12(a) is a multidimensional scaling of pairwise distances derived from methylation levels assayed on a custom array. FIG. 13(b) is a multidimensional scaling of pairwise distances derived from average methylation values in blocks identified via bisulfite sequencing. FIG. 13(c) is a plot of methylation values for normal, cancer and two adenoma samples.

FIG. 14 is a graphical plot of average log gene expression values, obtained from GEO dataset GSE8671, plotted versus the average difference in methylation of a nearby small DMR.

FIG. 15 is a graphical plot of across-sample standard deviation of methylation level for each block of normal versus cancer samples. Average methylation levels were computed for each block using high frequency smoothed SOLiD™ bisulfite sequencing data. The solid line is the identity line; CpGs above this line have greater variability in cancer.

FIG. 16 is a series of graphical plots. FIG. 16(a) is a plot of methylation values for cancer samples and normal samples with hypomethylated block locations highlighted (shading) plotted against genomic location. FIG. 16(b) plots standardized log expression values for 26 hypervariable genes in cancer located within hypomethylated block regions.

FIG. 17 is a graphical plot of standardized log expression values for 26 hypervariable genes in cancer located within hypomethylated block regions.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is based on the discovery that generalized loss of stability of epigenetic domains was determined to be a characteristic across various cancer types. A different and more general approach to cancer epigenetics is discussed herein based, in part on the recent observation of frequent methylation alterations in colon cancer of lower cytosine-density CpG regions near islands, termed shores; as well as the observation that these cancer-specific differentially methylated regions (cDMRs), correspond largely to the same regions that show DNA methylation variation among normal spleen, liver, and brain, or tissue-specific DMRs (tDMRs)⁴. Furthermore, these same cDMRs are highly enriched among regions differentially methylated during stem cell reprogramming of induced pluripotent stem (iPS) cells⁵. Thus it was reasoned that the very same sites might be generalized cDMRs, since they are involved in normal tissue differentiation but show aberrant methylation in at least one cancer type (colon).

Before the present compositions and methods are described, it is to be understood that this invention is not limited to the particular composition, method, and experimental conditions described, as such composition, method, and conditions may vary. It is also to be understood that the terminology used herein is for purposes of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only in the appended claims.

As used in this specification and the appended claims, the singular forms “a”, “an”, and “the” include plural references unless the context clearly dictates otherwise. Thus, for example, references to “the method” includes one or more methods, and/or steps of the type described herein which will become apparent to those persons skilled in the art upon reading this disclosure and so forth.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the invention, the preferred methods and materials are now described.

The hypothesis was tested by designing a semi-quantitative custom array for methylation analysis of cDMRs consistently altered across colon cancer, and analyzing these sites in 290 samples, including matched normal and cancer from colon, breast, lung, thyroid, and Wilms' tumor. As described below, it was surprisingly discovered that almost all of the cDMRs were altered across all cancers tested. Specifically, the cDMRs appeared to display an increased stochastic variation in methylation level, suggesting a generalized disruption of the integrity of the cancer epigenome. To investigate this idea further, genome-scale bisulfite sequencing of 3 colorectal cancers, the matched normal colonic mucosa, and two adenomatous polyps was performed. These experiments revealed a surprising loss of methylation stability in colon cancer, involving both CpG islands and shores, as well as large (up to several megabases) blocks of hypomethylation affecting more than half of the genome, with concomitant stochastic variability in gene expression.

As such, in one aspect, a method for detecting cancer or a risk of cancer in a subject is provided. The method includes detecting the methylation status of a genome from a nucleic acid containing sample from the subject, wherein hypomethylation or hypermethylation of at least 50% or more of the genome is indicative of cancer or a risk of cancer, thereby detecting cancer or a risk thereof.

In one embodiment, hypomethylation of at least 50% or more of the genome is indicative of cancer. For example, hypomethylation of at least 50, 55, 60, 65, 70, 75, 80, 85, 90, 95 or more of the genome is indicative of cancer.

In various embodiments, the methylation status is determined of one or more nucleic acid sequences selected from a differentially methylated region (DMR) as set forth in Table 16 or Table 17, wherein the one or more nucleic acid sequences are stochastically methylated in cancer. In another embodiment, the method includes detecting the methylation status of one or more nucleic acid sequences selected from a differentially methylated region (DMR) as set forth in Table 10, wherein the one or more nucleic acid sequences are stochastically methylated in cancer. In one embodiment, the method includes detecting the methylation status of one or more nucleic acid sequences selected from a genomic block region as set forth in Table 4, wherein the one or more nucleic acid sequences are stochastically methylated in cancer.

Hypomethylation is present when there is a measurable decrease in methylation. In some embodiments, a DMR or block can be determined to be hypomethylated when less than 50% of the methylation sites analyzed are not methylated. Hypermethylation is present when there is a measurable increase in methylation. In some embodiments, a DMR or block can be determined to be hypermethylated when more than 50% of the methylation sites analyzed are methylated. Methods for determining methylation states are provided herein and are known in the art. In some embodiments methylation status is converted to an M value. As used herein an M value, can be a log ratio of intensities from total (Cy3) and McrBC-fractionated DNA (Cy5): positive and negative M values are quantitatively associated with methylated and unmethylated sites, respectively. M values are calculated as described in the Examples. In some embodiments, M values which range from −0.5 to 0.5 represent unmethylated sites as defined by the control probes, and values from 0.5 to 1.5 represent baseline levels of methylation.

In various embodiments, a genome is present in a biological sample taken from a subject. The biological sample can be virtually any biological sample, particularly a sample that contains RNA or DNA from the subject. The biological sample can be a tissue sample which contains about 1 to about 10,000,000, about 1000 to about 10,000,000, or about 1,000,000 to about 10,000,000 somatic cells. However, it is possible to obtain samples that contain smaller numbers of cells, even a single cell in embodiments that utilize an amplification protocol such as PCR. The sample need not contain any intact cells, so long as it contains sufficient biological material (e.g., protein or genetic material, such as RNA or DNA) to assess methylation status of the one or more DMRs.

In some embodiments, a biological or tissue sample can be drawn from any tissue that is susceptible to cancer. A biological or tissue sample may be obtained by surgery, biopsy, swab, stool, or other collection method. In some embodiments, the sample is derived from blood, plasma, serum, lymph, nerve-cell containing tissue, cerebrospinal fluid, biopsy material, tumor tissue, bone marrow, nervous tissue, skin, hair, tears, fetal material, amniocentesis material, uterine tissue, saliva, feces, or sperm. In particular embodiments, the biological sample for methods of the present invention can be, for example, a sample from colorectal tissue, or in certain embodiments, can be a blood sample, or a fraction of a blood sample such as a peripheral blood lymphocyte (PBL) fraction. Methods for isolating PBLs from whole blood are well known in the art. In addition, it is possible to use a blood sample and enrich the small amount of circulating cells from a tissue of interest, e.g., colon, breast, lung, prostate, head and neck, etc. using a method known in the art.

As disclosed above, the biological sample can be a blood sample. The blood sample can be obtained using methods known in the art, such as finger prick or phlebotomy. Suitably, the blood sample is approximately 0.1 to 20 ml, or alternatively approximately 1 to 15 ml with the volume of blood being approximately 10 ml.

In one embodiment, the identified cancer risk is for colorectal cancer, and the biological sample is a tissue sample obtained from the colon, blood, or a stool sample. In another embodiment, the identified cancer risk is for stomach cancer or esophageal cancer, and the tissue may be obtained by endoscopic biopsy or aspiration, or stool sample or saliva sample. In another embodiment, the identified cancer risk is esophageal cancer, and the tissue is obtained by endoscopic biopsy, aspiration, or oral or saliva sample. In another embodiment, the identified cancer risk is leukemia/lymphoma and the tissue sample is blood. In another embodiment, the identified cancer risk is breast cancer, and the tissue is obtained by breast, blood, or nipple aspiration sample. In another embodiment, the identified cancer risk is breast cancer, and the tissue is obtained by breast, blood, or nipple fluid or aspiration sample. In another embodiment, the identified cancer risk is lung cancer, and the tissue is obtained by lung, blood, endoscopic biopsy or aspirate sample. In another embodiment, the identified cancer risk is thyroid cancer, and the tissue is obtained by thyroid, blood, or endoscopic biopsy sample. In another embodiment, the identified cancer risk is kidney cancer, and the tissue is obtained by thyroid, blood, or endoscopic biopsy sample.

In the present invention, the subject is typically a human but also can be any mammal, including, but not limited to, a dog, cat, rabbit, cow, bird, rat, horse, pig, or monkey.

As mentioned above, for certain embodiments of the present invention, the method is performed as part of a regular checkup. Therefore, for these methods the subject has not been diagnosed with cancer, and typically for these present embodiments it is not known that a subject has a hyperproliferative disorder, such as a cancer.

Methods of the present invention identify a risk of developing cancer for a subject. A cancer can include, but is not limited to, colorectal cancer, esophageal cancer, stomach cancer, leukemia/lymphoma, lung cancer, prostate cancer, uterine cancer, breast cancer, skin cancer, endocrine cancer, urinary cancer, liver cancer, thyroid cancer, kidney cancer (Wilms), pancreas cancer, other gastrointestinal cancer, ovarian cancer, cervical cancer, head cancer, neck cancer, and adenomas.

A hyperproliferative disorder includes, but is not limited to, neoplasms located in the following: abdomen, bone, breast, digestive system, liver, kidney, pancreas, peritoneum, endocrine glands (adrenal, parathyroid, pituitary, testicles, ovary, thymus, thyroid), eye, head and neck, nervous (central and peripheral), lymphatic system, pelvic, skin, soft tissue, spleen, thoracic, and urogenital. In certain embodiments, the hyperproliferative disorder is a cancer.

In another embodiment, the present invention provides a method for managing health of a subject. The method includes performing the method for identifying an increased risk of developing cancer discussed above and performing a traditional cancer detection method. For example a traditional cancer detection method can be performed if the method for identifying cancer risk indicates that the subject is at an increased risk for developing cancer. Many traditional cancer detection methods are known and can be included in this aspect of the invention. The traditional cancer detection method can include, for example, one or more of chest X-ray, carcinoembryonic antigen (CEA) level determination, colorectal examination, endoscopic examination, MRI, CAT scanning, or other imaging such as gallium scanning, and barium imaging, and sigmoidoscopy/colonoscopy, a breast exam, or a prostate specific antigen (PSA) assay.

In another embodiment, a method for providing a prognosis for cancer is provided. The method includes a) comparing the methylation status of one or more nucleic acid sequences in a sample from a subject diagnosed with, or being treated for cancer, to a methylation status of the one or more nucleic acid sequences of a cancer cell; and b) determining a prognosis based on the comparison of (a), wherein the one or more nucleic acid sequences are selected from the group consisting of a nucleic acid sequence as set forth in Table 4, Table 10, Table 16 and Table 17, thereby providing a prognosis for the cancer. In one embodiment, the method further includes detecting expression of one or more genes as set forth in FIG. 16A, FIG. 16B, Table 3 or Table 5.

In another aspect, a method for providing a profile of cancer is provided. The method includes a) comparing the methylation status of one or more nucleic acid sequences in a putative cancer cell from a subject, to a known methylation status of the one or more nucleic acid sequences of a cancer cell; and b) determining a methylation profile for the putative cancer cell based on the comparison of (a), wherein a stochastic variation in methylation status is indicative of the putative cancer cell being cancerous, and wherein further the one or more nucleic acid sequences are selected from a nucleic acid sequence as set forth in Table 4, Table 10, Table 16 and Table 17. In one embodiment, the method further includes detecting expression of one or more genes as set forth in FIG. 16A, FIG. 16B, Table 3 or Table 5.

Numerous methods for analyzing methylation status of a gene are known in the art and can be used in the methods of the present invention to identify either hypomethylation or hypermethylation of a genomic region. In some embodiments, the determining of methylation status is performed by one or more techniques selected from the group consisting of a nucleic acid amplification, polymerase chain reaction (PCR), methylation specific PCR, bisulfite pyrosequenceing, single-strand conformation polymorphism (SSCP) analysis, restriction analysis, and microarray technology. As illustrated in the Examples herein, analysis of methylation can be performed by bisulfite genomic sequencing. Bisulfite treatment modifies DNA converting unmethylated, but not methylated, cytosines to uracil. Bisulfite treatment can be carried out using the METHYLEASY bisulfite modification kit (Human Genetic Signatures).

In some embodiments, bisulfite pyrosequencing, which is a sequencing-based analysis of DNA methylation that quantitatively measures multiple, consecutive CpG sites individually with high accuracy and reproducibility, may be used. Nucleic acid primers or probes for such analysis may be derived from any of the Tables included herein or any other known genomic sequence.

It will be recognized that depending on the site bound by the primer and the direction of extension from a primer, that the primers listed above can be used in different pairs. Furthermore, it will be recognized that additional primers can be identified within the genomic regions identified in the Tables, especially primers that allow analysis of the same methylation sites as those analyzed with primers that correspond to the primers disclosed herein or any other known genomic sequence.

Altered methylation can be identified by identifying a detectable difference in methylation. For example, hypomethylation can be determined by identifying whether after bisulfite treatment a uracil or a cytosine is present a particular location. If uracil is present after bisulfite treatment, then the residue is unmethylated. Hypomethylation is present when there is a measurable decrease in methylation.

In an alternative embodiment, the method for analyzing methylation can include amplification using a primer pair specific for methylated residues within a genomic region, such as a DMR or block. In these embodiments, selective hybridization or binding of at least one of the primers is dependent on the methylation state of the target DNA sequence (Herman et al., Proc. Natl. Acad. Sci. USA, 93:9821 (1996)). For example, the amplification reaction can be preceded by bisulfite treatment, and the primers can selectively hybridize to target sequences in a manner that is dependent on bisulfite treatment. For example, one primer can selectively bind to a target sequence only when one or more base of the target sequence is altered by bisulfite treatment, thereby being specific for a methylated target sequence.

Other methods are known in the art for determining methylation status, including, but not limited to, array-based methylation analysis and Southern blot analysis.

Methods using an amplification reaction, for example methods above for detecting hypomethylation or hyprmethylation, can utilize a real-time detection amplification procedure. For example, the method can utilize molecular beacon technology (Tyagi S., et al., Nature Biotechnology, 14: 303 (1996)) or Taqman™ technology (Holland, P. M., et al., Proc. Natl. Acad. Sci. USA, 88:7276 (1991)).

Also methyl light (Trinh B N, Long T I, Laird P W. DNA methylation analysis by MethyLight technology, Methods, 25(4):456-62 (2001), incorporated herein in its entirety by reference), Methyl Heavy (Epigenomics, Berlin, Germany), or SNuPE (single nucleotide primer extension) (See e.g., Watson D., et al., Genet Res. 75(3):269-74 (2000)). Can be used in the methods of the present invention related to identifying altered methylation of DMRs.

As used herein, the term “selective hybridization” or “selectively hybridize” refers to hybridization under moderately stringent or highly stringent physiological conditions, which can distinguish related nucleotide sequences from unrelated nucleotide sequences.

As known in the art, in nucleic acid hybridization reactions, the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (for example, relative GC:AT content), and nucleic acid type, i.e., whether the oligonucleotide or the target nucleic acid sequence is DNA or RNA, can be considered in selecting hybridization conditions. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter. Methods for selecting appropriate stringency conditions can be determined empirically or estimated using various formulas, and are well known in the art (see, for example, Sambrook et al., supra, 1989).

An example of progressively higher stringency conditions is as follows: 2×SSC/0.1% SDS at about room temperature (hybridization conditions); 0.2×SSC/0.1% SDS at about room temperature (low stringency conditions); 0.2×SSC/0.1% SDS at about 42° C. (moderate stringency conditions); and 0.1×SSC at about 68° C. (high stringency conditions). Washing can be carried out using only one of these conditions, for example, high stringency conditions, or each of the conditions can be used, for example, for 10 to 15 minutes each, in the order listed above, repeating any or all of the steps listed.

The degree of methylation in the DNA being assessed, may be measured by fluorescent in situ hybridization (FISH) by means of probes which identify and differentiate between genomic DNAs, associated regions being assessed, which exhibit different degrees of DNA methylation. FISH is described in the Human chromosomes: principles and techniques (Editors, Ram S. Verma, Arvind Babu Verma, Ram S.) 2nd ed., New York: McGraw-Hill, 1995, and de Capoa A., Di Leandro M., Grappelli C., Menendez F., Poggesi I., Giancotti P., Marotta, M. R., Spano A., Rocchi M., Archidiacono N., Niveleau A. Computer-assisted analysis of methylation status of individual interphase nuclei in human cultured cells. Cytometry. 31:85-92, 1998 which is incorporated herein by reference. In this case, the biological sample will typically be any which contains sufficient whole cells or nuclei to perform short term culture. Usually, the sample will be a tissue sample that contains 10 to 10,000, or, for example, 100 to 10,000, whole somatic cells.

Additionally, as mentioned above, methyl light, methyl heavy, and array-based methylation analysis can be performed, by using bisulfite treated DNA that is then PCR-amplified, against microarrays of oligonucleotide target sequences with the various forms corresponding to unmethylated and methylated DNA.

The term “nucleic acid molecule” is used broadly herein to mean a sequence of deoxyribonucleotides or ribonucleotides that are linked together by a phosphodiester bond. As such, the term “nucleic acid molecule” is meant to include DNA and RNA, which can be single stranded or double stranded, as well as DNA/RNA hybrids. Furthermore, the term “nucleic acid molecule” as used herein includes naturally occurring nucleic acid molecules, which can be isolated from a cell, as well as synthetic molecules, which can be prepared, for example, by methods of chemical synthesis or by enzymatic methods such as by the polymerase chain reaction (PCR), and, in various embodiments, can contain nucleotide analogs or a backbone bond other than a phosphodiester bond.

The terms “polynucleotide” and “oligonucleotide” also are used herein to refer to nucleic acid molecules. Although no specific distinction from each other or from “nucleic acid molecule” is intended by the use of these terms, the term “polynucleotide” is used generally in reference to a nucleic acid molecule that encodes a polypeptide, or a peptide portion thereof, whereas the term “oligonucleotide” is used generally in reference to a nucleotide sequence useful as a probe, a PCR primer, an antisense molecule, or the like. Of course, it will be recognized that an “oligonucleotide” also can encode a peptide. As such, the different terms are used primarily for convenience of discussion.

A polynucleotide or oligonucleotide comprising naturally occurring nucleotides and phosphodiester bonds can be chemically synthesized or can be produced using recombinant DNA methods, using an appropriate polynucleotide as a template. In comparison, a polynucleotide comprising nucleotide analogs or covalent bonds other than phosphodiester bonds generally will be chemically synthesized, although an enzyme such as T7 polymerase can incorporate certain types of nucleotide analogs into a polynucleotide and, therefore, can be used to produce such a polynucleotide recombinantly from an appropriate template.

In another aspect, the present invention includes kits that are useful for carrying out the methods of the present invention. The components contained in the kit depend on a number of factors, including: the particular analytical technique used to detect methylation or measure the degree of methylation or a change in methylation, and the one or more genomic regions being assayed for methylation status.

In another aspect, a plurality of nucleic acid sequences is provided, useful as primers or probes. The nucleic acid sequences are capable of selectively hybridizing to a nucleic acid sequence selected from cancer-specific differentially methylated regions (cDMRs) as set forth in Table 17, wherein the cDMRs are stochastically methylated in cancer. In one embodiment, each nucleic acid sequence is about 10-55 base pairs in length.

To examine DNAm on a genome-wide scale, comprehensive high-throughput array-based relative methylation (CHARM) analysis, which is a microarray-based method agnostic to preconceptions about DNAm, including location relative to genes and CpG content was carried out. cDMRs identified in Irizarry et al.¹, and shown in Tables 14 and 15, including regions consistently differentially methylated in colon cancers were studied by comprehensive high-throughput array based methylation (CHARM) analysis. Probes were designed around CpGs that showed consistent differences in CHARM, while passing quality control metrics. The resulting probes covered 139 regions, with 1-7 probes per region. The majority of the probes were in CpG island shores (66%), defined as less than 2 kb away from the edge of a canonically defined high-CpG density island¹. The remainder of the probes were either inside CpG islands (11%) or >2 kb distant (23%). The resulting quantitative measurements of DNAm, denoted with M, are log ratios of intensities from total (Cy3) and McrBC-fractionated DNA (Cy5): positive and negative M values are quantitatively associated with methylated and unmethylated sites, respectively. The CHARM results were also extensively corroborated by quantitative bisulfite pyrosequencing analysis.

As such, in another aspect, a microarray is provided which includes the plurality of nucleic acid sequences as described herein. Further, in another aspect, a method of performing methylation analysis of genomic DNA isolated from a cell. The method includes performing comprehensive high-throughput array for relative methylation (CHARM) analysis an a sample of labeled, digested genomic DNA isolated from the cell using the microarray described herein, thereby performing methylation analysis.

Provided herein is a genome-wide analysis of DNA methylation of various cancer cells, revealing several surprising epigenomic observations. Surprisingly, two thirds of all methylation changes in colon cancer involve hypomethylation of large blocks comprising more than half of the genome. The most variably expressed genes in cancer are extraordinarily enriched in the blocks, and they involve genes associated with tumor heterogeneity and progression, including three matrix metalloproteinase genes, MMP3, MMP7, and MMP10, and a fourth, SIM2, which acts through metalloproteinases to promote tumor invasion. Another, STCI1, helps mediate the Warburg effect of reprogramming tumor metabolism. CHI3L1 encodes a secreted glycoprotein associated with inflammatory responses and poor prognosis in multiple tumor types including the colon. WISP genes are targets of Wnt-1 and are thought to contribute to tissue invasion in breast and colon cancer. One cautionary note raised by these findings is that treatment of cancer patients with nonspecific DNA methylation inhibitors could have unintended consequences in the activation of tumor-promoting genes in hypomethylated blocks.

The following example is provided to further illustrate the advantages and features of the present invention, but are not intended to limit the scope of the invention. While they are typical of those that might be used, other procedures, methodologies, or techniques known to those skilled in the art may alternatively be used.

Example 1 Generalized Loss of Stability of Epigenetic Domains Across Cancer Types

The following experimental protocols and materials were utilized.

Custom Array Design.

Custom bead arrays were created based on the 151 most statistically significant cDMRs identified in Irizarry et al.⁴ for which successful design probes using the Illumina protocol⁷ could be designed. Cryogenically stored freshly frozen samples were obtained from the Cooperative Human Tissue Network (NCI, Bethesda, Md.), the National Wilms Tumor Study tissue bank (Edmonton, Alberta, Canada) and the Johns Hopkins Hospital, under an IRB-approved waiver of consent. A pathologist validated classification of all samples independently and blindly. Samples were used for DNA purification, the resulting DNA bisulfite treated, and the custom GoldenGate assay performed. The raw intensity data was processed using quantile normalization²⁸ and ruled out batch effects following the procedures described by Leek et al.²⁹. Differences in variance were tested using a standard F-test.

Custom Methylation Array Processing and Analysis.

The raw intensity data from the Cy5 and Cy3 channels representing methylated and umethylated DNA was quantile normalized² separately, and methylation level was calculated as the ratio of the Cy5 intensity over the sum of the intensities from both channels. To control for array quality, arrays for which the average of the median log intensities from the two channels was small (<7), or for which the median absolute deviation of the overall methylation signal was small (<1.9) were removed from the dataset. Differences in methylation variability were measured and tested using an F-test. Differences in mean methylation levels were measured and tested using a t-test. Significance was taken as 0.01.

Illumina HumanMethylation27k™ Array Analysis.

A publicly available dataset was downloaded of methylation levels of 22 matched colon normal/tumor samples assayed using Illumina's HumanMethylation27 K™ array (Gene Expression Omnibus accession number GSE17648). The methylation measurements were used with no further preprocessing. Differences in methylation variability were measured and tested using an F-test. Differences in mean methylation levels were measured and tested using a t-test. Significance was taken as 0.01.

Whole Genome Bisulfite Sequencing.

Bisulfite sequencing libraries were prepared using the approach previously described by Bormann Chung et al³⁰, with some modifications so the entire protocol is provided in detail here. 5 ug of genomic DNA was sheared using a Covaris E2 sonicator. 40 ng of Alul-digested unmethylated A DNA was added to each sample in order to monitor the efficiency of bisulfite conversion. Sample DNA ends were then repaired using 1× End Polish Buffer, 400 nM each of dATP, dGTP and dTTP (leaving out dCTP), 40 U of End Polishing Enzyme 1 (Life Tech) and 80 U of End Polishing Enzyme 2 (Life Tech). Adaptor sequences, as detailed by Bormann Chung et al.³, were then ligated onto the samples, using 1×T4 ligase buffer, 4.5 uM of methyl-protect PI adaptor, 4.5 uM of P2 adaptor and 50 U of T4 ligase. Nick translation was performed in IX Exo-Klenow buffer, 0.5 mM dNTPs containing methyl dCTP and 20 units of Exo-Klenow-Fragment (Ambion) for 1 hour at 16° C. 500 ng aliquots of the resulting product was then bisulfite converted using formamide as an additional denaturant⁴. 24 uL of formamide was added to an equal volume of DNA and incubated at 95° C. for 5 minutes. Subsequently, 100 uL of Zymo Gold bisulfite conversion reagent (Zymo) was added, and the mixture was incubated for 8 hours in 50° C. Samples were then desulphonated and purified using spin columns following the EZ-DNA Zymo Methylation-Gold protocol. 5 uL of the bisulfite converted library was amplified in 1×PCR buffer, 0.2 mM dNTP, 1 mM each of the standard SOLiD™ fragment library primers, 5 U of Taq (Denville), and 0.25 U of Pfu Turbo Taq (Stratagene). The DNA was subjected to 8 cycles of PCR and the resulting product was purified using AMpure™ SPRI beads (Beckman Genomics). The libraries were then sequenced on the SOLiD™ 3+ platform yielding 50 base pair reads. Corresponding colon cancer and normal mucosa samples were sequenced simultaneously in adjacent flow cells.

Alignment of SOLiD™ Sequencing Reads from Bisulfite-Treated DNA.

A custom alignment tool for SOLiD™ reads was developed from bisulfite-treated DNA. Reads were aligned with the aid of a spaced-seed index of the genome while biasing neither toward nor against methylated cytosines in CpGs described previously³¹ to work with reads from SOLiD™ 3 Plus instruments. Note that aligners can introduce a bias when an unmethylated C (which becomes a T) is penalized for aligning to a C in the genome, but a methylated C (which remains a C) is not. The opposite bias can also occur, e.g., if all CpGs are converted to TpGs in the reference prior to alignment. Other projects address this in part by additionally converting Cs to Ts in the reads. But this approach is not applicable to the colorspace reads generated by the SOLiD™, for which nucleotide positions encoding Cs cannot be accurately determined prior to alignment. The aligner used here leaves each read as-is but penalizes neither C-to-C norT-to-C partial alignments in CpGs.

For alignment the approach taken by the BSMAP tool was extended. The approach used supports a broad range of spaced-seed designs and extends the BSMAP approach to additionally allow alignment of SOLiD™ colorspace reads. C/T bias is avoided by creating and storing multiple copies (potentially) of each reference subsequence indexed, one copy for each distinct assignment of Cs and Ts to genomic Cs or CpGs present in the subsequence. For colorspace reads, the algorithm extracts subsequences of colors (rather than nucleotides), and a copy it created for every distinct assignment of Cs and Ts to genomic Cs present in any nucleotide overlapped by any color in the extracted subsequence.

For these experiments, the alignment algorithm is configured to remove the penalty associated with either a C or a T aligning to a C in a CpG, and to treat non-CpG Cs in the genome as Ts. This policy removes bias from CpG methylation measurements, but assumes that there is little or no non-CpG cytosine methylation. Where non-CpG cytosine methylation occurs, this approach is more likely to fail to find alignments overlapping the methylated cytosine, and the resulting consensus will contain an anti-methylation bias at the methylated cytosine.

The algorithm was used to align a total of 7.79 billion reads obtained from 8 runs of a SOLiD™ 3 Plus instrument against a reference sequence collection consisting of the GRCh37 human genome assembly (including mitochondrial DNA and “unplaced” contigs) plus the sequence of the spiked-in phage genome. Each read obtained from the SOLiD™ 3 Plus instrument consists of a primer nucleotide followed by a string of 50 “colors,” where each color encodes a class of dinucleotides according to the SOLiD™ colorspace encoding scheme. Prior to alignment, the initial primer base and 5′-most color were trimmed from all input reads, yielding a string of 49 colors. The alignment policy was selected to guarantee that all alignments with up to 3 color mismatches would be found, and some but not all alignments with 4-6 color mismatches would be found. The alignment of a T or C to a C in a CpG does not incur a mismatch penalty (except in some cases where a sequencing error is also present). The policy was also set to distinguish between reads that align uniquely and those that align non-uniquely.

Color-to-color alignments are decoded into nucleotide alignments with a Viterbi-like algorithm. The final alignment, when expressed in nucleotides, is one character shorter than the input read, i.e. 48 nucleotides long. Alignments for reads aligning non-uniquely are ignored in subsequent stages. Alignment results are summarized in Table 1 and FIG. 1.

For the data of Table 1, alignment was performed against a collection of reference sequences consisting of the GRCh37 human genome assembly, including mitochondrial DNA and “unplaced” contigs, plus the sequence of the spiked-in A DNA. A read is said to align “uniquely” if it has exactly one valid alignment to the reference according to the alignment policy. A read is said to align “non-uniquely” if it has more than one valid alignment according to the alignment policy. A read “fails” to align if it has zero valid alignments. Cytosine conversion percentage is estimated as the fraction of high-quality evidence from unique A phage alignments indicating lack of methylation.

FIG. 1 shows the number of reads and alignments obtained from SOLiD™ 3+ bisulfite sequencing. The stacked bar chart illustrates the number of reads sequenced per flowcell, with the colors indicating uniquely reads, unaligned reads and non-uniquely aligned reads. A total of 7.79 billion reads were obtained from 8 runs (16 flowcells) of a SOLiD™ 3+ instrument.

After alignment, a series of scripts extract and summarize CpG methylation evidence present in the unique alignments. The evidence is compiled into a set of per-sample, per-chromosome evidence tables. Alignments to the A phage genome are also compiled into a separate table. A piece of CpG “evidence” is created when an alignment overlaps the cytosine position of a CpG in the reference and the overlapping nucleotide in the alignment is either a T (indicating a lack of methylation) or a C (indicating presence of methylation). Once a piece of evidence is extracted from a unique alignment, it is subjected to a filter. The filter removes evidence that is either refuted by one or both of the overlapping colors from the original read, or is within 4 positions of either end of the nucleotide alignment. All evidence that passes the filter is added to the CpG summary table. A record in the table summarizes, for a given CpG: the filtered evidence nucleotides that aligned to it, the filtered quality values (i.e. of the two colors overlapping the evidence nucleotide) that aligned to it, the number of distinct alignment positions from which filtered evidence was taken, the “mapability” of the CpG and surrounding bases (i.e. the number of 50-mers overlapping the CpG that are unique up to 3 mismatches), (e) the local CG content of the bases surrounded the CpG. The mapability measure for each genome position is pre-calculated using Bowtie⁸.

Table 2 summarizes the amount and type of evidence extracted at each stage. For Table 2, a piece of CpG evidence occurs when an alignment overlaps the cytosine position of a CpG in the reference sequence and the overlapping alignment nucleotide is either a T (indicating a lack of methylation) or a C (indicating presence of methylation). A filter is applied to remove nucleotide evidence that (a) is refuted by one or both of the overlapping colors from the original read, or (b) is within 4 positions of either end of the nucleotide alignment.

Table 3 summarizes the resulting CpG evidence coverage with respect to the GRCh37 human genome assembly for each sample. For Table 3, each sample is sequenced on two flowcells of a SOLiD™ 3+ instrument; here, results are calculated after pooling evidence from the two flowcells.

Finally, Table 4 summarizes per-sample average coverage both genome-wide and for CpG cytosines. For Table 4, average coverage of mappable CpG cytosines (column 3) is calculated by dividing the total number of pieces of C and T nucleotide evidence aligning to CpG cytosines after filtering (column 2) by the total number of CpG dinucleotides in GRCh37 that are “mappable” in the experiment: 20.9 million. A CpG is considered “mappable” if it is overlapped by at least one non-ambiguous reference 50 bp substring; non-ambiguous substrings are those for which no other 50 bp reference substring exists within 3 mismatches.

Evidence from reads that aligned uniquely to the λ genome were used to estimate the bisulfite conversion rate for unmethylated cytosines. The conversion rate is estimated as the fraction of high-quality evidence from reads aligning uniquely to the λ phage genome that indicates lack of methylation. FIG. 2 and the final column of Table 2 show the estimates, which all lie between 99.7% and 99.8%.

FIG. 2 shows the estimated unmethylated cytosine conversion rate per sample. Bisulfite conversion efficiency is plotted per SOLiD™ 3+ flowcell. Conversion efficiency is estimated as the fraction of high-quality evidence aligning to CpG cytosines in the unmethylated λ phage genome that indicates lack of methylation.

To measure global prevalence of non-CpG cytosine methylation, all filtered nucleotide evidence overlapping non-CpG cytosine positions in the human reference genome were examined. Filtered nucleotide evidence consists of evidence (a) from reads that aligned uniquely, (b) where both overlapping colors from the original read agree with the decoded nucleotide and, (c) where nucleotides within 4 positions of either end of the alignment are excluded. For each subject the overall fraction of evidence at CpG cytosine positions where the overlapping nucleotide is a T or a C. The same was done for non-CpG cytosine positions were measured. Table 5 summarizes the results, comparing them with the rate of cytosine non-conversion estimated from filtered evidence aligning to the λ phage genome.

For Table 5, the differentially expressed genes comparing colon cancer samples to normal samples were divided into two groups: those associated hypomethyiated boundary shifts and the rest. The table shows the five categories that with statistically significant enrichment (FDRO.01). It was observed that for all subjects, the fraction of Cs observed overlapping non-CpG cytosines does not rise above the approximate fraction expected from unconverted cytosines.

FIG. 3 shows the results of a simple diagnostic to assess the basic accuracy of the filtered evidence from the reads that aligned uniquely to the human genome. FIG. 3 shows SOLiD™ 3+ read position bias in evidence for methylation. The horizontal axis represents an offset into the nucleotide alignment from the 5′ end. The vertical axis represents the fraction of filtered CpG methylation evidence from that offset that indicates that methylation is present. Only reads aligning uniquely to the GRCh37 human genome assembly are considered.

The diagnostic is to calculate, for each alignment position (1 through 48), the proportion of filtered evidence taken from that position that indicates that methylation is present. In a perfect assay, this proportion should be independent of position, and the plot should trace a straight horizontal line. In practice, the lines are not flat due to sequencing error and other noise arising from sample preparation and alignment. The relative flatness of the lines obtained for the samples gives us some assurance that the signal obtained is not substantially affected by noise such as sequencing error. Note that, while this plot shows the proportion in all alignment positions, evidence from the first four and last four positions of the alignment was additionally filtered.

After alignment, reads with a quality score of 10 or less filtered out before smoothing the methylation data (next section).

Reads were mapped to CpGs and determined if they were evidence for methylated or unmethylated cytosines. These data were then processed with the local likelihood approach, which resulted in pair-wise correlations between methylation estimates for the three normal samples of 0.97, 0.96, and 0.96.

DMR Detection.

A smoothing approach was developed, based on local likelihood estimation³³, which leveraged the fact that the methylation status of neighboring CpG is highly correlated³⁴ to greatly improve precision of methylation measurements. Two related approaches; one for blocks and one for small DMRs was developed.

The alignment algorithm described in the previous section provided two counts for each CpG: number of pieces of filtered evidence indicating presence of methylation (M) and number of pieces of filtered evidence indicating unmethylation (U). The sum of these two counts was the coverage N. It was assumed that for each CpG, M followed a binomial distribution with success probability p, equal to the true methylation level, and N trials. Thus, M/N provided a naive estimate of p with standard error (M/N)×(1−M/N)/VN. Note that N, the coverage, ranged from 0 to 18,090 with a sample mean of 5.8-6.2 (after excluding CpGs with no coverage in all samples). Precision was greatly improved by leveraging the fact that proximal CpG have similar methylation levels and using a smoothing technique similar to that used in CHARM.

Because the data was binomially distributed, local likelihood estimation was used. This approach assumes that the p(L), the methylation level at genomic location L, is a smooth function of L; in other words, that CpGs that are close have similar methylation levels. The local likelihood approach uses data within windows of predefined sizes to estimates p(L) and weighing data based on distance to L (based on a tricube kernel). In addition, the binomial model ensures that data points with high coverage receive greater weight. Two window sizes were defined to detect the two different types of DMRs; for the blocks, a large window to detect low frequency differences, and a smaller window to detect high frequency differences, the small DMRs.

For each sample, the smoothed data was evaluated on the same grid of data points termed “covered CpGs”, consisting of those CpGs where at least two normals samples had a coverage of at least 2.

For the small DMRs, the high-frequency analysis used a window size of 70 CpG or 1,000 bps; whichever generated a larger region. For the blocks, the low-frequency analysis used a window size of 500 CpGs or 2,000 basepairs; again whichever was larger. Note that the use of a tricube kernel ensures that data points far from the center of the window receive a smaller weight. This approach provided highly precise estimates of CpG methylation levels p(L) for each sample. The standard errors ranged from 0-0.11 (mean of 0.04) for the high frequency smoothing and 0.01-0.04 (mean 0.02) for low frequency. An example of the results from the high-frequency smoothing is provided as FIG. 4. FIG. 4 shows precise methylation estimates obtained by high-frequency smoothing. The circles represent the single CpG estimates of methylation, which are plotted against the CpG location. The areas of the circles are proportional to the coverage. The high-frequency smoothed values (described in detail in the Methods) are plotted as solid lines. Dashed lines represent 95% pointwise confidence intervals. The region shown in the bottom panel illustrates the statistical approach.

A method for finding differences based on t-statistics that take into account biological variability was then developed. The highly precise estimates of pi(L) for each sample i at each CpG location L was started with. The average difference between the three tumor samples and the three normal samples referred to as d(L) was obtained. To properly account for biological variability (FIG. 5) the standard error of d(L) using the normal samples was estimated.

FIG. 5 illustrates the need for biological replication for detecting DMRs. FIG. 5(a), in the left panel, methylation patterns for three normal samples (top lines) and matched cancers (bottom) are shown. The detected DMR is shaded in pink. In the right panel, the average methylation values within the DMR for the three paired samples is shown (normal in blue, cancer in red, the matched sample pairs indicated by numbers). A t-test for the difference between normal and cancer and obtained a p value of 0.0056 was performed. FIG. 5(b) shows the same analysis as (a) for a region in which if only normal-cancer pair 3 (thick lines) were analyzed, there would appear to be a methylation difference between cancer and normal. However, the p value when all three samples are compared is 0.52. Notice that the methylation estimates are very precise (standard error for points in right panel are <0.02). Therefore the differences seen are biological not technical, and will be seen regardless of the measurement technology.

Only the normal samples were used because as demonstrated, cancer samples are prone to high variability (FIG. 6). FIG. 6 shows the increased methylation variance of common CpG sites across human cancer types. Methylation levels measured at 384 CpG sites using a custom Illumina array exhibit an increase in across-sample variability in (a) colon, (b) lung, (c) breast, (d) thyroid, and (e) kidney (Wilms tumor) cancers. Each panel shows the across-sample standard deviation of methylation level for each CpG in normal and matched cancer samples. The solid line is the identity line; CpGs above this line have greater variability in cancer. The dashed line indicates the threshold at which differences in methylation variance become significant (F-test at 99% level). In all five tissue types, the vast majority of CpGs are above the solid line, indicating that variability is larger in cancer samples than in normal. Colors indicate the location of each CpG with respect to canonical annotated CpG islands. (f) Using the CpGs that showed the largest increase in variability hierarchical clustering was performed on the normal samples. The heatmap of the methylation values for these CpGs clearly distinguishes the tissue types, indicating that these sites of increased methylation heterogeneity in cancer are tissue-specific DMRs.

The standard error se[d(L)] was therefore estimated as σ(L)*V(2/3) with σ(L) the standard deviation of the Pi(L) for the three normal samples. To improve standard error estimates, these were smoothed using a running mean with a window size of 101 observations. To avoid inflated t-statistics as a result of artificially low variance, a threshold for the standard deviation of its 75th percentile was set, before computing the smoothed result. With the standard deviation in place the t-statistic t(L)=d(L)/se[d(L)] was constructed.

For the high frequency analysis the t-statistic was further corrected for low frequency changes. This allowed discovery of local features, such as a hypermethylated small DMR, inside global features, i.e. hypo- or hypermethylated block. This correction factor was calculated by forming a fixed grid of positions 2,000 bp apart in the genome, linearly interpolating the neighboring t-statistics to obtain measurements at these positions and then smoothing this dataset with a robust smoother based on the Huber family¹⁰ and a bandwidth of 25,000 bp. Small DMRs were then defined as contiguous CpGs within 300 bp of each other, with the t-statistics above 4.6 or below −4.6 (corresponding to the 95th quantile of the empirical distribution of the t-statistics) and all differences in the same direction. For the low frequency analysis the t-statistics cutoff was 2 and contiguous CpG were defined as within 10,000 bps from each other.

These sets of regions formed the small DMRs and blocks that were subsequently filtered and processed according to the following criteria. 1) A small DMR needed to contain at least 3 covered CpGs and have at least 1 covered CpG per 300 bp. Furthermore, the mean difference in methylation percentages between tumors and normals across the small DMR had to be greater than 0.1. 2) A block needed to be longer than 5 kb. Blocks containing CpG Islands with a mean methylation of less than 0.25 in the normal samples were separated into two. Putative blocks that were shorter than 5 kb were included as small DMRs provided they satisfied the small DMR filters above.

After filtering, pairs of small DMRs were merged if they were less than 1 kb apart, changed in the same direction (both hypermethylated or both hypomethylated), and had no covered CpGs in the area separating them. A partial list of blocks is shown as Table 6, and of small DMRs as Table 7. Additional blocks and small DMRs were determined which are not shown in Tables 6 and 7.

The data from the adenoma samples were smoothed in the same way.

DMR Classification.

Small DMRs were classified into categories based methylation profiles of the tumor and normal samples within the DMR and the two flanking regions (within 800 bp). Based on these results, the DMRs that were discovered from data exploration could be classified into three types termed loss of methylation boundaries, shifting of methylation boundaries, and novel hypomethylation (FIG. 7). FIG. 7 shows loss of epigenetic stability at small DMRs. Methylation estimates are plotted against genomic location for normal samples and cancer samples. The small DMR locations are shaded. Grey bars indicate the location of blocks, CpG islands, and gene exons. Tick marks along the bottom axis indicate the location of CpGs. Pictured are examples of (a) a methylation boundary shift outward (normal-top lines in shaded area; cancer-bottom lines in shaded area), (b) a methylation boundary shift inward (cancer-top lines in shaded area; normal-bottom lines in shaded area), (c) a loss of methylation boundary (cancer-top lines in shaded area; normal-bottom lines in shaded area), and (d) a novel hypomethylation DMR (normal-top lines in shaded area; cancer-bottom lines in shaded area).

A mathematical algorithm was used to automatically classify DMRs. Briefly, mean methylation was computed for both tumor and normal samples within the DMR and in the flanking the DMR both upstream and downstream. This provided three numbers for each of the six samples. If all the normal samples showed high methylation values (>50%) in the flanking regions and low methylation values (<0.25%) and the tumor samples all showed intermediate values across DMR and flanking regions, the DMR was classified as loss of methylation boundary. If one of the flanking regions had low methylation values in both the normal and the tumor samples, the region was classified as a shift of methylation boundary. Finally, if all the normal samples showed high methylation values in the DMR and flanking regions while the tumor samples were lower in the DMR, the region was classified as novel hypomethylation. The details of the algorithm are best understood by viewing the computer code (made available upon request).

Hypomethylation in Blocks and Repeat Regions.

Repeat regions were identified based on the UCSC repeatMasker track¹¹. Based on the repeats and/or blocks, the genome was segmented into regions both repeats and blocks, repeats but not blocks, not repeats but blocks, and neither repeats nor blocks. The methylation levels were computed as the average of the high-frequency smoothed methylation levels of all CpGs in the 4 different regions. Density estimates were computed from the same distribution.

Enrichment of Overlap Between Different Genomic Domains.

For each pair of different genomic domains (like blocks and LOCKs) a 2×2 table is formed containing the number of CpGs inside and outside the two genomic domains (like inside blocks and inside LOCKS, inside blocks and outside LOCKs, etc). Odds ratios and p-values were calculated using Fisher's exact text.

Copy Number Analysis.

Estimates of copy number were based on the per-base coverage obtained after alignment. The filters developed were not applied specifically for methylation measurements (described in the Bisulfite alignment Section). Note that the coverage considered here is not specific to CpGs: every genomic position is assigned a coverage value. For each sample, the average coverage in non-overlapping 10,000 bp windows was then computed, yielding two coverage vectors for each tumor-normal pair denoted cov(T) and cov(N). For each tumor-normal pair the corrected log-ratio: log 2(CN)=log 2(cov(T))−log 2(cov(N))+c was defined. Here c is a correction factor to account for different yields in each sequencing run; c is defined as the log of total sequencing yield of the normal sample divide by total yield of the tumor sample. The copy number log-ratios were segmented using circular binary segmentation (CBS)¹². For illustrative purposes, copy number log-ratios and the associated segmentation on chromosome 20 were depicted (FIG. 8a ).

To determine if copy number had an effect on methylation estimates, each segment provided by CBS was divided into 100 kb regions. For each of these regions average copy number ratios as well as average methylation ratios was computed. These were then plotted (FIG. 8b ) and no relationship between CNV and methylation blocks was observed.

FIG. 8 shows that block and small DMR detection not affected by copy number variation. For FIG. 8(a) for a 25 megabase region of chromosome 20 (1-25 MB), the methylation differences between all three normal-cancer pairs plotted along the chromosome, with red lines representing the average values in blocks are shown. Notice that the location of blocks is consistent across all three normal-cancer pairs. For illustrative purposed, highlighted (shade) are the seven largest blocks. For FIG. 8(b) for each normal-cancer pair, copy number alterations is shown, quantified by log ratios (base 2) of coverage in cancer sample to coverage in normal sample, for the same region as in (a). Log-ratios of 0 are associated with lack of copy number alternations in cancer, while values larger or equal to log₂(3/2) (dashed line) are associated with gain of copy number in cancer. The red lines represent segments obtained with the CBS algorithm (described in the Methods). Notice that each sample shows different copy number alterations. For FIG. 8(c) differences in methylation are plotted against differences in copy number (log-ratios) for the entire genome. Specifically, for each of the segments detected by CBS, the average difference in methylation and the average log-ratio associated with copy number alteration was computed. This was done for each sample and all the points combined in one scatter-plot.

Capture Bisulfite Sequencing.

Bisulfite Padlock Probes (BSPP) were used to capture bisulfite converted gDNA using a previously described method³². Sequencing libraries were generated from the captured DNA, and sequenced on an Illumina™ GA II instrument, generating 79.3 million reads. Capture reads were aligned using the same methodology as the whole genome bisulfite reads, but adapted to work in nucleotide space instead of color space.

Assays for Large Organized Chromatin K9-Modifications (LOCKs).

Primary human pulmonary fibroblasts (HPF) were purchased from ScienCell Research Laboratories (San Diego, Calif.). Cell culture was conducted using the media and protocols recommended by ScienCell. Primary cells at the second passage were used for H3K9Me2 LOCK analysis. ChIP-on-chip experiments and microarray data analysis were performed as described earlier¹².

Gene Expression Analysis.

Expression data was obtained from the gene expression barcode (rafalab.jhsph.edu/barcode). This resource combines all the expression data from the public repositories purportedly to standardize data in a way that allows one to call a gene expressed or not expressed. From this source, two independent colon cancer datasets (GSE8671³⁵ and GSE4183^(36,37)) were used. To define hypervariable genes an F-test using a across sample variance in tumor and normal samples computed from the original log expression was performed. A gene was defined as expressed if it had a gene expression barcode standardized value above 2.54 (p=0.01). For the fibroblast analysis datasets (GSE7890³⁸, GSE11418³⁹, GSE11919⁴⁰) were downloaded. These expression values from these datasets were also standardized using the gene expression barcode. The standardized values were used to determine if genes were expressed or not each sample.

To determine the correlation between small DMRs and expression, a gene and a small DMR were considered associated if the DMR was within 2,000 bps from the transcription start site of the gene; 6,869 genes mapped to a DMR in this way.

Data Annotation.

Annotation was obtained from the UCSC genome browser based on hgl9. In the cases where a data track was only available for hgl8 or hgl7, the UCSC liftOver tool was used to map between builds of the human genome. Specifically the repeatMasker track, the RefSeq mRNA track, and the UCSC known genes track were used.

Laminin Associated Domain (LAD) coordinates were obtained from the NKI LADs track from UCSC, generated from microarrays in fibroblast cells. PMDs were obtained from Lister et al., generated from bisulfite sequencing in fibroblast cells¹¹. DNase I hypersensitive sites were obtained from the UCSC ENCODE track, using the Hies, Caco2rep1, and Caco2rep2, both the narrow and broad peak.

Results

Stochastic variation in DNA methylation as a defining feature across cancer types.

It was desired to increase the precision of DNA over the previous tiling array-based approach, termed CHARM (Comprehensive High-throughput Array for Relative Methylation)⁶, analyzing 151 colon cDMRs from Irizarry et al.⁴. A custom nucleotide-specific bead array (see Methods) was designed on the type of Illumina GoldenGate™ platform previously shown to be quantitative within 6% of DNA methylation⁷. The resulting 384 probes covered 139 regions, with 1-7 probes per region. To test the generality of DNA methylation alterations across tumor types, 290 samples were studied, including cancers from colon (10), lung (24), breast (27), thyroid (36), and kidney (Wilms') (25), with matched normal tissues to 111 of these 122 cancers, as well as 30 colon premalignant adenomas, and an additional 18 normal colon and 9 normal breast samples. To minimize the risk of genetic heterogeneity arising from sampling multiple clones DNA from small (0.5 cm×0.2 cm) sections verified by histopathologic examination were purified.

Cluster analysis of the DNA methylation values revealed that the colon cancer cDMRs largely distinguished cancer from normal across tumor types (FIG. 9).

FIG. 9 shows that methylation levels of differentially methylated CpGs in colon cancer largely differentiate cancer from normal in colon(a), lung(b), breast(c), thyroid(d) and kidney(e)(Wilms) tissues. Columns and rows in each panel are ordered by a hierearchical clustering of methylation profiles using Euclidean distance. The heights of dendrogram branches, larger between tumor samples than between normal samples, illustrate the increased across-sample variability in cancer seen in a majority of CpGs in all tissues.

Even more striking than the differences in mean methylation between cancer and normal was the increased across-sample methylation variability in the cancer samples compared to normal, within each type, but occurring generally across all cancer types (FIG. 9). Therefore the across-sample variance within normal and cancer samples in all five tumor/normal tissue types at each CpG site was computed. For each tissue type, the great majority of CpGs exhibited greater variance in cancer than normal (FIG. 6(a)-(e)), even though these sites had been selected for differences in mean values in colon cancer. This increase was statistically significant (p<0.01, using an F-test) for 81%, 92%, 81%, 70%, and 80% of the CpG sites in colon, lung, breast, thyroid, and Wilms' tumor, respectively. Furthermore, 157 CpG sites had statistically significant increased variability in all cancer types tested. This increased stochastic variation was found in CpG islands, CpG island shores, and regions distant from islands (FIG. 6(a)-(e)). This increased methylation variability in cancer are not themselves due to mean differences because the cancers show marked departure in variation from the expected binomial distribution that is followed in the normal samples. These data suggest a potential mechanism of tumor heterogeneity, namely increased stochastic variation of DNA methylation in cancers compared to normal, within each tumor type tested (see Discussion).

To rule out artifactual methylation heterogeneity caused by a greater degree of cell type heterogeneity in cancers compared to normal, a careful histological analysis for cellular subtypes within all of the colon and kidney tumor and normal samples was performed by a board-certified oncology pathologist. The normal samples were on average much more heterogeneous than the tumor samples in cellular composition. Thus, the data showing greater methylation variability in cancers cannot be due to increased cellular heterogeneity in the cancers compared to normal. This increased variation was not due to patient age, as the great majority of the samples were normal/tumor matched, and an age-corrected analysis did not change the result.

To address a potential connection between genetic and epigenetic heterogeneity that might underlie the data two experiments were performed. First, five Wilms tumor samples were selected which showed little to no intertumoral genetic variation by microarray-based copy number analysis and compared them to five colon cancers which showed relatively high amounts of copy number variation. Similar levels of methylation hypervariability were present in both types of cancers despite the differences in copy number variation. Second, immunohistochemical staining was performed for aberrant p53 expression on sections taken from Wilms tumor and colon cancers (7 samples of each), since p53 expression is a marker of chromosomal instability in both of these types of cancer. All seven colon samples tested positive for aberrant p53 whereas none of the Wilms tumors were positive. Analysis of these same samples by a custom GoldenGate™ arrays showed similar levels of methylation hypervariability in both of these cancer types, despite differential expression of p53.

These same loci which show increased variability in cancer are also able to distinguish the normal tissues from each other, but this is a mean shift rather than a variation shift, apparent from cluster analysis. Interestingly, even using a reduced set of the 25 sites which are most variable in cancer the five normal tissue types are clearly discriminated from each other (FIG. 6(f)). This result reinforces the concept of a biological relationship between normal tissue differentiation and stochastic variation in cancer DNA methylation.

To determine if the increased variability is a general property of cytosine methylation in cancer or a specific property of the CpGs selected for the custom array, as a control a publicly available methylation dataset comparing colorectal cancer to matched normal mucosa on the Illumina HumanMethylation™ 27 k beadchip array was used. In this dataset it was found that only 42% of the sites showed a statistically significant increase in methylation variability, compared to 81% in the custom array (p<0.01), confirming the specificity of the cancer DMRs included in the custom array. Examining variability with respect to location relative to CpG islands, it was noted that increased stochastic variation was more common in CpGs far from islands (57%) than in shores (44%) or islands (31%), contrasting the relative representation of these locations on the 27 k array which breaks down as: distal to islands (26.4%), shores (31.6%) and islands (42%) (see Methods). This was an intriguing result as it suggested that something other than relationship to CpG islands might be defining the largest fraction of sites of altered DNA methylation in cancer.

Hypomethylation of Large DNA Methylation Blocks in Colon Cancer.

The methylation stochasticity described above appears to be a general property of cancer, affecting cDMRs in both island and non-island regions, in all five cancer types tested. To further investigate this apparent universal loss of DNA methylation pattern integrity in cancer, and to analyze the lower CpG abundance regions not previously examined by array-based methods, shotgun bisulfite genome sequencing on 3 colorectal cancers and the matched normal colonic mucosa from these three patients using the ABI SOLiD™ platform was performed. Methylation estimates with enough precision to detect differences as small as 10% methylation were desired. Because a local likelihood approach was used, which aggregated information from neighboring CpGs, and combined data from 3 biological replicates, it was determined that 4× coverage would suffice to estimate methylation values at the desired precision with a standard error of at most 3% (See Methods for details). Between 12.5 and 13.5 gigabases of data for each sample was therefore obtained, which after quality control filtering (see Methods) provided ˜5× coverage for each CpG after aligning the bisulfite converted read (Table 4). After statistical processing, pair-wise correlations were obtained between methylation estimates for the three normal samples of 0.97, 0.96, and 0.96, confirming the adequacy of sequencing coverage. Details on the mapping and statistical algorithms are available in the Methods Section.

To verify the accuracy of the methylation values obtained via the local likelihood approach, capture bisulfite sequencing was performed on the same 6 samples that were sequenced, for 39,262 regions which yielded 39.3 k-125.6 k CpG with >30× coverage. These results showed a correlation of 0.82-0.91 between the local likelihood approach and the capture bisulfite sequencing, a remarkable agreement given that the experiments were performed in different laboratories using different sequencing platforms and different protocols. Close examination of individual loci demonstrated that the methylation estimates closely track the high-coverage capture data. While capture bisulfite sequencing is far more exhaustive and CpG inclusive, traditional bisulfite pyrosequencing was further performed, which also confirmed the accuracy of the approach.

The bisulfite sequencing analysis revealed the surprising presence of large blocks of contiguous relative hypomethylation in cancer compared to normal (FIGS. 10(a)-(b)). FIG. 10 shows the existence of large hypomethylated genomic blocks in human colon cancer. Shown in (a) and (b) are smoothed methylation values from bisulfite sequencing data for cancer samples (red) and normal samples (blue) in two genomic regions. The hypomethylated blocks are shown with pink shading. Grey bars indicate the location of PMDs, LOCKs, LADs, CpG Islands, and gene exons. Note that the blocks coincide with the PMD, LOCKS, and LADs in panel (a) but not in (b). (c) The distribution of methylation values for the normal samples (blue) versus the cancer samples (red) demonstrates global hypomethylation of cancer compared to normal. (d) The distribution of methylation values in the blocks (solid lines) and outside the block (dashed lines) for normal samples (blue) and cancer samples (red). Note that while the normal and cancer distributions are similar outside the blocks, within the blocks methylation values for cancer exhibit a general shift. (e) Distribution of methylation differences between cancer and normal samples stratified by inclusion in repetitive DNA and blocks. Inside the blocks, the average difference was ˜20% in both in repeat and non-repeat areas. Outside the blocks, the average difference was ˜0% in repeat and non-repeat areas, indicating that blocks rather than repeats account for the observed differences in DNA methylation.

13,540 such regions of median size 39 kb, varying from 5 kb-10 MB were identified (partial listing in Tables 6 and 8). The across-cancer average loss of mean DNA methylation throughout all the blocks was 12%-23% (partial listing shown in Table 6). Remarkably, these hypomethylated blocks in cancer corresponded to more than half of the genome, even when accounting for the number of CpG sites within the blocks (Table 8). Analysis shows that these blocks are common across all three cancers; an analysis of the tumors individually versus a normal profile shows consistent block boundary locations (see FIG. 10, FIG. 2, and Methods). The existence of a small fraction of hypermethylated blocks (3% of all differentially methylated blocks) in cancer was also noted, with examples visible on the far right edge of FIG. 10(a) and FIG. 10(b) (Table 8). A histogram of smoothed methylation values shows the shift in distribution of global DNA methylation (FIG. 10(c)). The relatively small compartments of fully unmethylated or fully methylated changed little in the aggregate between normal and cancer. Instead, the predominant change in block methylation in cancer was a loss in the more abundant compartment of intermediate methylation levels (mean 73% for all samples) to a significantly less methylated level (50-61%). Examining methylation density distributions stratified by block and non-block regions supported this finding (FIG. 10(d)). It is important to note that copy number variation does not drive the results presented here. First, the locations of copy number variation changes in cancer, observed in the data, were not consistent across subjects, in contrast to the consistent locations of methylation changes in the blocks identified above. Second, the methylation difference estimates provided by the statistical approach did not correlate with copy number values.

Global quantitative hypomethylation in cancer⁸ is widely attributed to the presence of normally methylated repetitive elements⁹ and may be relevant to colon cancer as UNE-1 element hypomethylation is associated with worse prognosis in colon cancer¹⁰. It was observed that in normal tissues, repetitive elements were more methylated than non-repetitive regions (76% vs. 66%). To determine whether such repetitive elements were responsible for the block hypomethylation, differences in methylation levels inside and outside repeat elements (see Methods), both inside and outside the blocks were compared. It was clear from this analysis that most of the global hypomethylation was due to hypomethylated blocks (FIG. 10(e)) and not to the presence of repetitive elements. As repetitive elements are slightly enriched in blocks (odds ratio 1.4), much of the apparent repeat-associated methylation may in fact be due to blocks. This result does not exclude repeat-associated hypomethylation, since not all repeats were mappable. However, 57% of L1 elements, 94% of L2 elements, 95% of MIR sequences, and 18% of Alu elements were covered by the data (FIG. 11) and did not show repeat-specific hypomethylation (FIG. 4). It is important to note it is possible that Alu sequences not covered by the data are somehow more hypomethylated than covered Alu sequences, and thus would contribute to global hypomethylation.

FIG. 11 shows the methylation changes of selected repetitive DNA families. Distribution of methylation differences between cancer and normal samples stratified by repeat family and inclusion in blocks. CpGs outside all repetitive elements were used as controls. Each graph is the percentage of mappable CpGs in each repeat family.

Lister et al. recently performed bisulfite sequencing analysis of the H1 human embryonic stem cell line compared to the IMR90 fibroblast line, identifying large regions of the genome that are less methylated in fibroblast cells than ES cells, referred to as partially methylated domains (PMDs)¹¹. The intermediate-methylation level regions identified above largely coincided with the PMDs, containing 85% of CpGs inside PMDs (odds ratio 6.5, R<2×10⁻¹⁶, Table 9). Large organized chromatin lysine (K) modifications, or LOCKs, genome-wide in normal mouse cells, that are associated with both constitutive and tissue-specific gene silencing were previously described that ¹². Therefore LOCKs in primary human cells (see Methods) mapped and whether the LOCKs also correspond to the hypomethylated blocks was determined. Remarkably, 89% of the LOCKs were contained within the blocks (odds ratio 6.8, P<2×10⁻¹⁶). LOCKs are also known to overlap with nuclear lamina-associated domains or LADs¹². Approximately 83% of the LADs were also contained within the blocks, similar to the LOCKs (odds ratio 4.9, P<2×10⁻¹⁶). In addition, DNase I hypersensitive sites, a structural signal for regulatory regions¹³ were enriched within 1 kb of block boundaries and small DMRs (p<2×10⁻¹⁶ for both). Thus the large hypomethylated blocks identified in cancer correspond to a genomic organization identified in normal cells by several complementary methods. Note that although the PMDs and the hypomethylated blocks largely overlap, significant differences in gene expression in cancer between non-overlapping blocks and PMDs is demonstrated later.

Furthermore, a relationship between the hypervariable CpGs across all cancer types, from the custom Illumina™ array described above, and the hypomethylated blocks identified by whole genome bisulfite sequencing was observed. Because the custom array was designed to contain both hypomethylated and hypermethylated CpG sites tested for enrichment of these hypervariable 157 CpG sites in hypomethylated blocks and in the small number of hypermethylated blocks. It was found that 63% of the hypomethylated hypervariable CpGs were indeed within hypomethylated blocks, and 37% of the hypermethylated hypervariable CpGs were within the hypermethylated blocks. To test for statistical significance, these percentages were compared to those found for the CpGs in the HumanMethylation27K array CpGs that did not vary differently in cancer and normal. These percentages were 13% and 1.5% for the hypomethylated and hypermethylated blocks, respectively, demonstrating high statistical significance for enrichment of hypervariably methylated CpGs in blocks (p<2×10⁻¹⁶; Table 10).

Small DMRs in Cancer Involve Loss of Stability of DNA Methylation Boundaries.

A statistical algorithm (see Methods) was then developed for detecting consistent DNA methylation changes in regions smaller than the blocks (≤5 kb). Critical for this algorithm was the analysis of biological replicates, as it was found that regions showing across-subject variability in normal samples would otherwise be easily confused with DMRs if only one cancer-normal pair were available (FIG. 5). Methylation measurements in these smaller regions exhibited good agreement with methylation measurements in the previous CHARM-based microarray analysis⁴ (FIG. 12).

FIG. 12 shows a comparison of CHARM microarray data and bisulfite sequencing for measuring methylation in (a) normal and (b) cancer samples. Average methylation level from previously published CHARM microarray data (Irizarry et al. (2009)) (y-axis) is plotted versus the average methylation obtained from high-frequency smoothed bisulfite sequencing data. Each point represents one of the cDMR regions originally identified in (Irizarry et al. (2009)). Note the high degree of correlation between CHARM and sequencing.

These are referred to as small DMRs to distinguish them from the large (>5 kb) differentially methylated blocks described above. The increased comprehensiveness of sequencing over CHARM and other published array-based analyses allowed us to detect many more small DMRs than previously reported, 5,810 hypermethylated and 4,315 hypomethylated small DMRs (partial listing of DMRs shown in Table 7). Previous findings⁴ that hypermethylated cDMRs are enriched in CpG islands while hypomethylated cDMRs are enriched in CpG island shores were also confirmed (Table 8).

The increased comprehensiveness of sequencing also allowed us to quantify the different types of methylation changes at CpG Islands specifically (Table 11). It was found that: (1) 61% of islands were unmethylated in normal colon, and of these 17% showed a >10% absolute increase in methylation in cancer; (2) 20% of islands were found to be fully methylated in the normal colon, and of these 24% showed a >10% decrease in absolute methylation in cancer; and (3) 18% of islands show partial methylation in normal colon, and of these 17% showed increased and 36% decreased methylation in cancer. Of the 3907 hypermethylated small DMRs overlapping CpG Islands, 63.7% involved changes in either shift or loss boundary. Additionally, to determine if the same pattern held true for promoter, genic, intergenic, and repeat CpG islands analysis in Table 11 was stratified. It was found that in the normal samples promoter CpG Islands are largely unmethylated but that the findings above still hold. In contrast a balanced proportion of methylated and unmethylated (35% versus 26%) intergenic CpG islands with 45% hypomethylated in cancer was observed (Table 1).

When the architecture of the small DMRs was examined, the most common characteristic was a shift in one or both of the DNA methylation boundaries of a CpG island out of the island into the adjacent region (FIG. 7(a)) or into the interior of the island (FIG. 7(b)). Where the boundary shifts are observed, the same regions would appear on array-based data as hypermethylated islands, if the boundary is shifting into the island, or to hypomethylated shores, if the boundary is shifting outside the island.

The second most frequent category of small DMRs involved loss of methylation boundaries at CpG islands. For example, the architecture of many hypermethylated cDMRs were defined in normal samples by unmethylated regions (<10% methylation) surrounded by highly methylated regions (75-95% methylation), with boundaries ˜100 bp wide. In cancer, these regions exhibited an approximately constant methylation level of approximately 40-60% throughout (Table 8, FIG. 7(c)). These regions with loss of methylation boundaries largely correspond to what are typically classified as hypermethylated islands in cancer.

Hypomethylated cDMRs were also found that arose de novo in highly methylated regions outside of blocks. In these cases, regions in which normal colon tissue was 75-95% methylated dropped to lower levels (20-40%) in cancer (FIG. 7(d)). These regions are referred to as novel hypomethylated DMRs, and they usually corresponded to CpG-rich regions that were not conventional islands (Table 8). In summary, in addition to the hypomethylated blocks, 10,125 small DMRs were found, 5,494 of which clearly fell in three categories: shifts of methylation boundaries, loss of methylation boundaries, and novel hypomethylation. Note that not all small DMRs followed a consistent pattern across all three sample pairs and therefore did not permit their classification (Table 8).

Methylation-Based Euclidean Distances Show Colon Adenomas Intermediate Between Normals and Cancers.

By performing a multidimensional scaling of the methylation values measured via the custom array in each colon sample, it was observed that the normal samples clustered tightly together in contrast to the dispersed methylation values measured in the cancer samples (FIG. 13(a)). This is consistent with the observed increase in methylation variability found in cancer that was described earlier. 30 colon adenomas were also analyzed for methylation on the custom array, and found that the adenomas were intermediate in both variability within samples and distance to the cluster of normal samples (FIG. 13(a)).

FIG. 13 shows that adenomas show intermediate methylation variability. (a) Multidimensional scaling of pairwise distances derived from methylation levels assayed on a custom array. Note that cancer samples (red) are largely far from the tight cluster of normal samples (blue), while adenoma samples (black) exhibit a range of distances: some are as close as other normal samples, others are as far as cancer samples, and many are at intermediate distances. (b) Multidimensional scaling of pairwise distances derived from average methylation values in blocks identified via bisulfite sequencing. Matching sequenced adenoma samples (labeled 1 and 2) appear in the same locations relative to the cluster of normal samples in both (a) and (b). (c) Methylation values for normal (blue), cancer (red) and two adenoma samples (black). Adenoma 1, which appeared closer to normal samples in the multidimensional scaling analysis (a), follows a similar methylation pattern to the normal samples. However, in some regions (shaded with pink) differences between Adenoma 1 and the normal samples are observed. Adenoma 2 shows a similar pattern to cancers.

Whole genome bisulfite sequencing was then performed on two of these adenomas, a premalignant colon adenoma with relatively small methylation-based distance to the normal colons and an adenoma with a large methylation-based distance to the normal colons, similar to the cancer samples. For each adenoma, the average methylation levels in each block and used these values to compute pairwise Euclidean distances were then computed. These results, based on measurements from the hypomethylated blocks, confirm the characteristic described above for the bead array data: genome-wide increased variability in cancers compared to normals with adenomas exhibiting intermediate values (FIG. 13).

Expression of Cell Cycle Genes Associated with Hypomethylated Shores in Cancer.

Whole genome methylation analysis has shown an inverse relationship between gene expression and methylation, especially at transcriptional start sites¹⁴. To study the relationship between methylation and gene expression in small DMRs, public microarray gene expression data was obtained from cancer and normal colon samples (see Methods Section) and compared to results from the sequencing data. Each gene represented in the expression microarrays was mapped to the closest DMR. A gene and DMR were considered associated if the DMR was within 2 kb of the transcription start site of the gene; 6,869 genes mapped to a DMR in this way. The expected inverse relationship between DNA methylation and gene expression was observed (r=−0.27, p<2×10⁻¹⁶, FIG. 14).

FIG. 14 shows an inverse correlation of gene expression with methylation at small DMRs. Average log gene expression values, obtained from GEO dataset GSE8671, plotted versus the average difference in methylation of a nearby small DMR. A gene and a small DMR were considered associated if the DMR was within 2,000 bp of the transcription start site of the gene; 6,869 genes mapped to a DMR in this way. Different types of small DMRs are indicated by color, boundary shift (green), boundary loss (orange), novel hypomethylation (purple) and other (pink). The dashed lines represent a fold change of 2 in the gene expression comparison.

By examining the inverse relationship between methylation and gene expression for each category of small DMRs separately, the strongest relationship for hypomethylated shores due to methylation boundary shifts (Table 12) was noticed. Gene ontology enrichment analysis was performed for differentially expressed genes (FDR<0.05), comparing those associated with hypomethylated boundary shifts to the other categories. These categories (Table 13) were strongly enriched for cell-cycle related genes CEP55, CCNB1, CDCA2, PRC1, CDC2, FBXO5, AURKA, CDK1, CDKN3, CDK7, and CDC20B, among others (Table 14).

Increased Variation in Gene Expression in Hypomethylated Blocks and DMRs.

Given the increased DNA methylation variability in cancer found with the custom bead arrays (FIG. 6(a)-(e)), the methylation patterns in the blocks was examined and found increased variability in cancer as well. Specifically, across-subject methylation variability levels within the blocks in cancer and normal were compared, and found a striking similarity to the results found with the Illumina custom bead array as described above (FIG. 6(a)-(e) compared to FIG. 15).

FIG. 15 shows increased variation in methylation between normal and cancer samples in blocks. Across-sample standard deviation of methylation level for each block of normal versus cancer samples. Average methylation levels were computed for each block using high frequency smoothed SOLiD™ bisulfite sequencing data. The solid line is the identity line; CpGs above this line have greater variability in cancer. As in FIG. 6, the vast majority of blocks show an increased variation in cancer compared to normal samples.

To study the relationship to gene expression in colon cancer, public gene expression data was obtained from cancer and normal samples (see Methods Section). The expression data was processed with the gene expression barcode¹⁶, a statistical algorithm that leverages information from thousands of publicly available datasets to standardized expression measurements in a way that expression values for silenced genes follow a standard normal distribution (mean 0 and standard deviation 1). Note that while expression values reported in the public databases cannot be used to call genes silenced or expressed, the barcode approach permits the construction of statistical tests for silencing. Genes in the blocks were generally silenced (80% genes silenced in all samples) both in normal and cancer samples. Of the genes consistently transcribed in normal tissue, albeit at low levels, 36% are silenced in blocks in cancers, compared to 15% expected by chance. This is consistent with other reports in the literature, e.g. Frigola et al¹⁷.

More strikingly than subtle differences in gene silencing, substantial enrichment of genes exhibiting increased expression variability in cancer compared to normal samples in the hypomethylated blocks was found. First, the possibility that this observed increased variability was due to tissue-specific genes being over-represented in blocks and the potential high cellular heterogeneity of cancer by noting the lack of association between tissue-specific genes and cancer variability outside of the blocks was ruled out. A clear association between increased variability in expression of a gene and its location within a hypomethylated block was then noticed. For example, 26 of the 50 genes exhibiting the largest increase in expression variability were inside the blocks; 52% compared to the 17% expected by chance (p=3×10⁻⁹); and there is significant enrichment at P=0.01 up to as many as 1,000 genes of the 4,940 genes on the array and within the blocks. Expression levels for 25 of these 26 most hypervariable genes exhibited an interesting pattern: while never expressed in normal samples, they exhibited stochastic expression in cancer (FIGS. 16 and 17). For example the genes MMP3, MMP7, MMP10, SIM2, CHI3L1, STC1, and WISP (described in the Discussion) were expressed in 96%, 100%, 67%, 8%, 79%, 50%, and 17% of the cancer samples, respectively, but never expressed in normal samples (Table 14).

FIG. 16 shows high variability of gene expression associated with blocks. (a) An example of hypervariably expressed genes contained within a block, MMP7, MMP10, and MMP3 (red). Methylation values for cancer samples (red) and normal samples (blue) with hypomethylated block locations highlighted (pink shading) are plotted against genomic location. Grey bars are as in FIG. 8. (b) Standardized log expression values for 26 hypervariable genes in cancer located within hypomethylated block regions (normal samples in blue, cancer samples in red). Standardization was performed using the gene expression barcode. Genes with standardized expression values below 2.54, or the 99.5th percentile of a normal distribution (horizontal dashed line) are determined to be silenced by the barcode method¹⁵. Vertical dashed lines separate the values for the different genes. Note there is consistent expression silencing in normal samples compared to hypervariable expression in cancer samples.

FIG. 17 shows hypervariable gene expression in cancer in hypomethylated blocks. Standardized (using gene expression barcode) expression values for the 26 of the 50 most hypervariable genes in cancer which are within hypomethylated block regions. Genes with standardized expression values below 2.54 (dotted horizontal line) are determined to be silenced by the barcode method (Zilliox and Irizarry, 2007). Expression values for each gene, separated by vertical dotted lines, from dataset GSE4183 are plotted for normal (blue) and cancer (red) samples. Note there is consistent expression silencing in normal samples compared to variable expression in cancer samples.

Functional Differences Between Hypomethylated Blocks and PMDs.

As noted above, the hypomethylated blocks observed, substantially overlapped the PMDs previously reported in a fibroblast cell line by Lister et al.¹¹. The genomic regions that did not overlap between blocks and PMDs were therefore examined, in order to identify potential functional differences between them. They were grouped into two sets: 1) regions within the hypomethylated blocks not in the PMDs (B+P−) and 2) the counterpart regions within the PMDs but not in the hypomethylated blocks (B−P+). To examine the expression of genes within these regions, public microarray gene expression data from fibroblast samples was obtained (see Methods Section). As expected, the genes in the fibroblast PMDs were relatively silenced in the fibroblast samples; 79% of genes were silenced in all samples within the PMD compared to 49% outside, p<2×10⁻¹⁶). Furthermore, genes that were silenced in fibroblast samples and consistently expressed in colon were enriched in the B−P+ regions (odds ratio of 3.2, p<2×10⁻¹⁶), while genes consistently silenced in colon and consistently expressed in fibroblast samples were enriched in the B+P− regions (odds ratio 2.8, p=0.0004). B+P− and B−P+ genes were then examined with respect to expression variability in cancer, focusing on the 50 hypervariable genes described above. These genes were markedly enriched in the B+P− regions (p=0.00013), yet showed no enrichment in the B−P+ regions. These results suggest that hypervariable gene expression in colon cancer is related specifically to their presence in hypomethylated blocks.

Discussion

In summary, it is shown that colon cancer cDMRs are generally involved in the common solid tumors of adulthood, lung, breast, thyroid, and colon cancer, and the most common solid tumor of childhood, Wilms tumor, with tight clustering of methylation levels in normal tissues, and marked stochastic variation in cancers. Current efforts to exploit DNA methylation for cancer screening are focused on identifying a cancer-specific profile¹⁸, but the data shown here suggest that epigenetic variability per se may be pathognomonic for cancer. Future efforts might be directed at defining the cancer epigenome as the departure from a narrowly defined normal profile rather identifying a specific narrowly defined cancer profile.

Surprisingly, two-thirds of all methylation changes in colon cancer involve hypomethylation of large blocks, with consistent locations across samples, comprising more than half of the genome. The most variably expressed genes in cancer are extraordinarily enriched in the blocks, and they involve genes associated with tumor heterogeneity and progression, including three matrix metalloproteinase genes, MMP3, MMP7, and MMP10¹⁹, and a fourth, SIM2, which acts through metalloproteinases to promote tumor invasion²⁰. Another, STC1, helps mediate the Warburg effect of reprogramming tumor metabolism²¹. CHI3L1 encodes a secreted glycoprotein associated with inflammatory responses and poor prognosis in multiple tumor types including the colon²². WISP genes are targets of Wnt-1 and are thought to contribute to tissue invasion in breast and colon cancer²³. Gene ontology enrichment analysis¹⁵ was performed for genes associated with hypervariable expression in blocks (FDR<0.05), which showed substantial enrichment for categories including extracellular matrix remodeling genes (Table 13). One cautionary note raised by these findings is that treatment of cancer patients with nonspecific DNA methylation inhibitors could have unintended consequences in the activation of tumor-promoting genes in hypomethylated blocks. It is also important to note that previous studies^(24,25) have shown large-region hypermethylation or no regional methylation change, although the present study is based on whole-genome bisulfite sequencing.

The small DMRs, which while representing a relatively small fraction of the genome (0.3%), are numerous (10,125), and frequently involve loss of boundaries of DNA methylation at the edge of CpG islands, shifting of the DNA methylation boundaries, or the creation of novel hypomethylated regions in CG-dense regions that are not canonical islands. These data underscore the importance of hypomethylated CpG island shores in cancer. In particular, the large number of shores associated with hypomethylation and gene overexpression in cancer are enriched for cell cycle related genes, suggesting a role in the unregulated growth that characterizes cancer.

A model it proposed that might help to explain the relationship between tissue-specific DMRs and the sites of extreme methylation variability in cancer. Pluripotency itself might require a certain degree of stochastic gene expression at some loci, allowing for differentiation along alternative pathways in response to external stimuli, or even in part randomly. The epigenome could collaborate by changing its physical configuration to relax the stringency of epigenetic marks away from extremes near 100% and 0%, since variance increases away from the extremes. One potential way the epigenome may do this is by reducing the methylation of large blocks in cancer, which overlap with known functionally important domains, LOCKs and LADs, and thus could involve a change in the chromatin packing density or proximity to the nuclear lamina. Similarly, subtle shifts in DNA methylation boundaries near CpG islands may drive chromatin organization and normal tissue-specific and aberrant cancer-specific gene expression. Consistent with this idea, a shift in methylation boundary was shown to differentially regulate genes escaping X-inactivation²⁶. It will therefore be important in the future to relate the data presented here to large-scale chromatin organization, and to normal developmental changes in DNA methylation and chromatin, as well as to expand future epigenetic investigations on the boundaries of blocks and CpG island shores.

It is not argued that epigenetic changes in cancer arise independently of genetic changes; both are clearly important and they are highly inter-related. However, the increased methylation and expression variability in each cancer type, compared to the normal samples, is consistent with the potential selective value of increased epigenetic plasticity in a varying environment first suggested for evolution but equally applicable to the strong but variable selective forces under which a cancer grows, such as varying oxygen tension or metastasis to a distant site²⁷. Thus, increased epigenetic heterogeneity in cancer at cDMRs (which are shown also as tDMRs) could underlie the ability of cancer cells to adapt rapidly to changing environments, such as increased oxygen with neovascularization, then decreased oxygen with necrosis; or metastasis to a new intercellular milieu.

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Tables

The following is a listing of the Tables which form part of this specification.

TABLE 1 Sequencing and alignment results for the 7.79 billion bisulfite reads obtained from 8 runs (16 flowcells) of a SOLiD ™ 3+ instrument. Conversion Uniquely aligned percent (A Reads Unique Unaligned Non-unique to A phagze estimate) Normal 1 Flowcell 1 485,990,920 183,844,653 226,160,599 75,985,667 6,762,031 99.7789 Normal 1 Flowcell 2 491,108,959 180,074,869 235,598,979 75,435,110 6,974,109 99.7807 Tumor 1 Flowcell 1 495,809,693 185,828,257 233,836,993 76,144,442 8,526,067 99.7456 Tumor 1 Flowcell 2 482,952,465 178,456,624 230,494,869 74,000,971 8,122,750 99.7472 Normal 2 Flowcell 1 496,397,317 180,791,619 237,818,636 77,787,061 7,270,350 99.7646 Normal 2 Flowcell 2 503,561,286 182,437,294 242,263,685 78,860,306 7,538,526 99.7657 Tumor 2 Flowcell 1 497,625,604 187,406,059 232,909,571 77,309,973 8,251,881 99.7804 Tumor 2 Flowcell 2 494,805,108 184,876,404 233,935,851 75,992,852 8,261,281 99.7860 Normal 3 Flowcell 1 489,558,995 168,584,119 251,409,912 69,564,963 8,817,079 99.7953 Normal 3 Flowcell 2 495,129,950 185,140,655 234,292,582 75,696,712 9,550,241 99.7937 Tumor 3 Flowcell 1 491,209,978 170,520,921 249,977,651 70,711,405 7,104,618 99.7919 Tumor 3 Flowcell 2 475,735,953 179,289,913 222,767,391 73,678,648 7,295,636 99.7930 Adenoma 1 Flowcell 1 477,819,340 153,546,992 259,594,989 64,677,358 3,457,741 99.7684 Adenoma 1 Flowcell 2 474,211,342 149,570,667 260,639,196 64,001,478 3,337,933 99.7678 Adenoma 2 Flowcell 1 479,069,565 165,738,601 242,575,131 70,755,832 12,991,935 99.7021 Adenoma 2 Flowcell 2 458,864,972 150,866,083 244,060,513 63,938,375 10,969,639 99.7055 Total 7,789,851,447 2,786,973,730 3,838,336,548 1,164,541,153 125,231,817 N/A Average 486,865,715 174,185,858 239,896,034 72,783,822 7,826,989 99.7667

TABLE 2 Methylation evidence results for the 831 million bisulfite reads that aligned uniquely to the GRCh37 human genome assembly and overlapped at least one CpG cytosine. Reads Filtered providing Raw pieces of pieces of Filtered evidence Filtered evidence % CpGs covered by human CpG human CpG human CpG Indicating presence indicating lack of £1 piece of filtered evidence evidence evidence of methylation methylation evidence Normal 1 Flowcell 1 54,178,356 74,924,756 68,839,724 48,253,347 20,586,377 65.158% Normal 1 Flowcell 2 53,689,203 74,623,785 68,199,772 47,773,815 20,425,957 65.045% Tumor 1 Flowcell 1 55,834,653 77,831,608 71,498,083 45,243,596 26,254,487 65.103% Tumor 1 Flowcell 2 53,902,278 75,253,470 68,697,400 43,321,299 25,376,101 64.479% Normal 2 Flowcell 1 54,492,135 76,436,939 70,022,135 49,881,756 20,140,379 65.797% Normal 2 Flowcell 2 55,012,691 77,239,693 70,641,796 50,296,004 20,345,792 65.978% Tumor 2 Flowcell 1 55,815,773 77,542,380 71,153,086 42,104,541 29,048,545 65.526% Tumor 2 Flowcell 2 54,867,691 76,121,856 69,486,614 40,787,828 28,698,786 65.271% Normal 3 Flowcell 1 50,056,580 70,114,583 63,620,050 43,447,381 20,172,669 64.004% Normal 3 Flowcell 2 54,385,230 75,777,367 69,162,172 47,580,371 21,581,801 65.333% Tumor 3 Flowcell 1 51,426,265 71,942,006 65,509,795 35,741,629 29,768,166 63.954% Tumor 3 Flowcell 2 53,527,518 74,427,549 68,200,974 37,298,457 30,902,517 64.356% Adenoma 1 Flowcell 1 47,841,436 67,596,302 61,069,078 40,572,495 20,496,583 63.580% Adenoma 1 Flowcell 2 46,522,581 65,753,563 59,413,620 39,519,156 19,894,464 63.125% Adenoma 2 Flowcell 1 46,102,652 63,325,754 58,045,004 33,949,586 24,095,418 61.767% Adenoma 2 Flowcell 2 43,224,022 59,918,936 54,862,907 32,006,566 22,856,341 60.444% Total 830,879,064 1,158,830,547 1,058,422,210 677,777,827 380,644,383 N/A Average 51,929,942 72,426,909 66,151,388 42,361,114 23,790,274 64.308%

TABLE 3 Coverage per sample in terms of fraction of CpGs in the GRCh37 human genome assembly covered by at least one through ten pieces of filtered evidence. Percent of CpGs in human genome covered with filtered evidence at depth > threshold Threshold Normal 1 Tumor 1 Normal 2 Tumor 2 Normal 3 Tumor 3 Adenoma 1 Adenoma 2 1 73.395% 73.279% 73.934% 73.636% 73.555% 72.994% 73.062% 71.459% 2 64.399% 63.918% 65.169% 64.567% 63.869% 63.247% 62.381% 60.906% 3 56.813% 56.119% 57.880% 57.091% 55.734% 55.099% 53.244% 51.613% 4 49.137% 48.461% 50.469% 49.640% 47.684% 47.116% 44.372% 42.406% 5 41.348% 40.917% 42.832% 42.148% 39.706% 39.335% 35.876% 33.569% 6 33.796% 33.753% 35.286% 34.872% 32.115% 32.000% 28.103% 25.573% 7 26.804% 27.219% 28.188% 28.088% 25.232% 25.391% 21.338% 18.770% 8 20.635% 21.496% 21.847% 22.042% 19.270% 19.674% 15.731% 13.296% 9 15.442% 16.658% 16.446% 16.862% 14.321% 14.917% 11.282% 9.114% 10 11.254% 12.693% 12.040% 12.596% 10.369% 11.087% 7.892% 6.061%

TABLE 4 Per-sample total coverage both genome- wide and for CpG cytosines. Total # Cs, Average Total Ts aligning to CpG coverage of genome coverage cytosines after mappable CpG after filtering filtering cytosines Normal 1 13,213,005,428 116,394,219 5.578 Tumor 1 13,106,826,609 118,994,714 5.703 Normal 2 13,137,358,383 119,303,310 5.717 Tumor 2 13,411,947,895 119,273,248 5.716 Normal 3 12,592,027,592 113,220,232 5.426 Tumor 3 12,593,520,085 113,929,959 5.460 Adenoma 1 10,965,839,892 102,341,491 4.905 Adenoma 2 11,017,476,026  95,652,482 4.584

TABLE 5 Gene ontology enrichment analysis of differentially expressed genes associated with hypomethylated boundary shifts. Expected Odds Gene ontology term count Count Size ratio P-value Q-value Mitotic cell cycle 11.6 31 185 3.1 3.8 × 10′″ 0.00036 Cell cycle process 18.7 42 297 2.6 5.4 × 10′″ 0.00036 Mitosis 9.9 25 157 2.9 1.5 × 10* 0.006 Positive regulation of ubiquitin-protein ligase 3.9 14 61 4.5 2.0 × 10″⁵ 0.0071 activity during mitotic cell cycle Organelle fission 13.7 30 216 2.5 3.6 × 10″⁶ 0.0097

TABLE 6 Partial listing of all blocks. Mean Normal Direction of Number of Mean Difference in Block Methylation Methylation Block Chromosome Start End Length (bp) Covered CpGs (Normal to Cancer) in Block Change Identifier # chr5 21489059 31186536 9697478 37675 −0.234268134 0.734330205 hypo Block: 4543 chr11 36593009 43333410 6740402 25948 −0.24463665 0.72048786 hypo Block: 9693 chr13 53781664 57714588 3932925 13954 −0.305545997 0.711763715 hypo Block: 11148 chr21 22381968 26930794 4548827 18960 −0.2505675 0.756884964 hypo Block: 15290 chr2 80539743 84644887 4105145 16332 −0.267703723 0.759607379 hypo Block: 1907 chr13 80942533 84441763 3499231 12625 −0.298381103 0.746321237 hypo Block: 11199 chr13 64409368 67804582 3395215 13021 −0.307076261 0.738041828 hypo Block: 11158 chr4 31837743 36042235 4204493 15647 −0.241796633 0.745280322 hypo Block: 3920 chr4 62080875 66522493 4441619 15678 −0.215135077 0.727287561 hypo Block: 4022 chr13 88335260 91331372 2996113 11498 −0.317647884 0.746888186 hypo Block: 11205 chr14 82002535 85986581 3984047 16771 −0.237315369 0.732144115 hypo Block: 11690 chr1 186650123 190431798 3781676 13581 −0.239010595 0.730909343 hypo Block: 1093 chr2 139542344 142876253 3333910 13078 −0.271062506 0.730863885 hypo Block: 2253 chr13 67805561 70681708 2876148 10486 −0.312824914 0.741708123 hypo Block: 11159 chr6 101857270 105211359 3354090 11778 −0.265353657 0.718599696 hypo Block: 5932 chr8 110991321 114435951 3444631 12032 −0.249961594 0.726061396 hypo Block: 7777 chr4 27027813 30714427 3686615 15174 −0.233244635 0.732405787 hypo Block: 3918 chr6 64781914 68135922 3354009 11651 −0.254436718 0.742306268 hypo Block: 5815 chr13 103537996 106379735 2841740 14762 −0.299969882 0.75065476 hypo Block: 11280 chr4 135122912 139025858 3902947 14280 −0.216279595 0.731078219 hypo Block: 4261 chr8 103515636 107003349 3487714 13016 −0.241256516 0.770620255 hypo Block: 4846 chr2 145284315 148597827 3313513 13133 −0.250369967 0.768882073 hypo Block: 2263 chr5 162945693 166400217 3454525 15949 −0.236434257 0.743274302 hypo Block: 5162 chr11 79160629 82433198 3272570 13761 −0.249348956 0.741907936 hypo Block: 9922 chr16 58772443 62060450 3288008 13991 −0.246684267 0.718572681 hypo Block: 12754 chr7 51385467 54287005 2901539 13679 −0.275190877 0.748760802 hypo Block: 6651 chr16 62080456 65149968 3069513 13481 −0.256640701 0.733695903 hypo Block: 12756 chr9 29226108 32382722 3156615 11467 −0.249093612 0.731939294 hypo Block: 8015 chr3 101813882 105080396 3266515 12243 −0.240181749 0.731165345 hypo Block: 3257 chr1 104303555 107593269 3289715 11541 −0.23823305 0.72189185 hypo Block: 707 chr3 81815567 84995827 3180261 12053 −0.245526983 0.722332842 hypo Block: 3219 chr6 91326051 94116126 2790076 10822 −0.268202124 0.718064341 hypo Block: 5907 chr1 79126358 82259961 3133604 12403 −0.237925127 0.743040164 hypo Block: 604 chr2 50583698 53900730 3317033 13801 −0.22375074 0.736886578 hypo Block: 1751 chr2 33830244 36578497 2748254 11175 −0.267193673 0.748361203 hypo Block: 1661 chr8 136654697 139508773 2854077 14571 −0.254392188 0.728932573 hypo Block: 7864 chr13 61995910 64396288 2400379 8579 −0.299834016 0.724209953 hypo Block: 11157 chrX 85414815 88460052 3045238 9748 −0.2314649 0.691151077 hypo Block: 16142 chr2 115926233 118572016 2645784 10906 −0.265411244 0.744511161 hypo Block: 2128 chr11 24518888 27204558 2685671 9942 −0.259298873 0.719126267 hypo Block: 9649 chrX 92939359 95917227 2977869 9693 −0.229421228 0.715510287 hypo Block: 16168 chr12 59990530 62574045 2583516 8746 −0.260909378 0.736280652 hypo Block: 10512 chr10 106407888 108914052 2506165 11609 −0.267129648 0.727394012 hypo Block: 9300 chrX 125623341 128646623 3023283 9673 −0.220628914 0.680113668 hypo Block: 16272 chr7 8491816 10972334 2480519 9599 −0.266486025 0.731347171 hypo Block: 6419 chr3 93844458 96523914 2679457 9264 −0.244848019 0.749307746 hypo Block: 3231 chr4 96481198 99064573 2583376 8631 −0.253163018 0.771246185 hypo Block: 4142 chr21 19619152 22361288 2742137 11521 −0.237643624 0.735566502 hypo Block: 15289 chr11 96438151 98891492 2453342 9261 −0.260094762 0.736211041 hypo Block: 9971 chr3 164922858 167395863 2473006 8723 −0.25282541 0.728991946 hypo Block: 3569 chr5 83689571 86368465 2678895 9231 −0.232430302 0.734591762 hypo Block: 4793 chr13 84465407 86760270 2294864 8967 −0.270969783 0.744753069 hypo Block: 11201 chr5 18724044 21326444 2602401 9227 −0.236011523 0.728125296 hypo Block: 4541 chr13 58216167 60245957 2029791 8263 −0.302398366 0.736161101 hypo Block: 11151 chr11 82997567 85330225 2332659 8797 −0.262715066 0.750980029 hypo Block: 9926 chrX 25044753 27938276 2893524 10823 −0.210432677 0.69002005 hypo Block: 15922 chr8 114455735 116660311 2204577 8460 −0.275918809 0.760219929 hypo Block: 7778 chr3 162545744 164854376 2308633 7528 −0.26187185 0.751854969 hypo Block: 3567 chr8 82757802 85082598 2324797 8122 −0.259271201 0.732975303 hypo Block: 7663 chrX 120120740 122716511 2595772 9115 −0.232007342 0.696660353 hypo Block: 16266 chr8 2075841 4842451 2766611 23658 −0.217001119 0.747948445 hypo Block: 7279 chr2 21266995 23605857 2338863 11850 −0.255865544 0.744975472 hypo Block: 1569 chr7 108217612 110648801 2431190 8810 −0.245305894 0.745758531 hypo Block: 6973 chrX 97112870 99651996 2539127 8276 −0.233209651 0.701125869 hypo Block: 16172 chr14 42090762 44858143 2767382 9153 −0.213661689 0.751157265 hypo Block: 11469 chr18 25765038 28557567 2792530 10654 −0.208293299 0.732008432 hypo Block: 13796 chr4 178373228 180974533 2601306 11690 −0.22356313 0.74760807 hypo Block: 4408 chr9 104504246 106855909 2351664 8348 −0.246985287 0.712364561 hypo Block: 8388 chr10 54882137 57367947 2485811 9209 −0.231717077 0.726408164 hypo Block: 8998 chr2 122525765 124771883 2246119 10811 −0.254626436 0.742716913 hypo Block: 2167 chr7 145833098 148036419 2203322 11206 −0.257545498 0.741253435 hypo Block: 7162 chr14 45729749 48134117 2404369 8507 −0.231616334 0.743704513 hypo Block: 11474 chr12 16556035 19048774 2492740 9971 −0.222688407 0.741387585 hypo Block: 10279 chrX 31285029 33741131 2456103 12249 −0.222790713 0.71239725 hypo Block: 15929 chr3 20235490 22413466 2177977 8565 −0.25102724 0.731377306 hypo Block: 2920 chr14 27076164 29220955 2144792 7582 −0.253990664 0.745559366 hypo Block: 11415 chr4 161308668 164025969 2717302 10275 −0.199998113 0.734277673 hypo Block: 4363 chr14 86008725 88447418 2438694 10658 −0.222147798 0.729272346 hypo Block: 11692 chr6 139925122 142404629 2479508 9214 −0.218090162 0.773113438 hypo Block: 6130 chr10 83643326 85899009 2255684 9719 −0.238429087 0.717901237 hypo Block: 9135 chr18 39683477 42254337 2570861 9558 −0.208077845 0.726480785 hypo Block: 13842 chr2 211343341 213393136 2049796 8062 −0.260670698 0.715032503 hypo Block: 2573 chr1 190452410 192505179 2052770 7275 −0.259681969 0.746636933 hypo Block: 1094 chr13 92051762 93866964 1815203 7386 −0.293411846 0.747627221 hypo Block: 11209 chrX 3855730 6130707 2274978 11389 −0.232508521 0.750302774 hypo Block: 15845 chr4 115618708 118006513 2387806 8414 −0.218711272 0.73447363 hypo Block: 4208 chr7 117970353 119906785 1936433 6581 −0.269548773 0.722954824 hypo Block: 7008 chr3 143720800 145789116 2068317 7390 −0.252294248 0.745173492 hypo Block: 3493 chr3 85024558 87039586 2015029 8042 −0.258692117 0.715713079 hypo Block: 3220 chr5 115916225 118236347 2320123 9563 −0.224129125 0.763312656 hypo Block: 4883 chr2 103457866 105456231 1998366 10688 −0.259016024 0.73603149 hypo Block: 2051 chr11 54786586 57043515 2256930 8679 −0.228713765 0.724414673 hypo Block: 9737 chr12 72675647 74917679 2242033 7398 −0.227951742 0.722874947 hypo Block: 10574 chr14 39911247 42065903 2154657 7118 −0.236850258 0.722983848 hypo Block: 11467 chr5 11914272 14011546 2097275 9183 −0.24321052 0.72539112 hypo Block: 4519 chr7 66804283 69056971 2252689 13569 −0.226275186 0.735389169 hypo Block: 6745 chr4 130273911 132671888 2397978 8289 −0.212562183 0.729529185 hypo Block: 4257 chr4 59789825 62054959 2265135 7865 −0.223670844 0.731342303 hypo Block: 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0.731937145 hypo Block: 15158 chr6 153458258 154718235 1259978 5928 −0.213976753 0.72863515 hypo Block: 6212 chr6 63015380 64282114 1266735 4702 −0.212737003 0.752126004 hypo Block: 5811 chr1 55685670 56897272 1211603 5636 −0.22238201 0.770802504 hypo Block: 512 chr3 147148365 148240383 1092019 3809 −0.246252898 0.73097331 hypo Block: 3499 chr1 68963027 70022986 1059960 3596 −0.252564575 0.707644962 hypo Block: 576 chr10 91597832 92609615 1011784 3771 −0.264402156 0.724010043 hypo Block: 9173 chr2 16689858 17656303 966446 4663 −0.276457392 0.713817408 hypo Block: 1545 chr16 51197459 52414402 1216944 6560 −0.219146475 0.688741631 hypo Block: 12699 chr8 46838903 48099795 1260893 9887 −0.211410253 0.741274767 hypo Block: 7505 chr5 166408484 167587319 1178836 7794 −0.22577032 0.737518333 hypo Block: 5163 chr8 60036941 61189713 1152773 4711 −0.229483099 0.817476517 hypo Block: 7557 chr14 25600783 26674085 1073303 4216 −0.245853638 0.716710063 hypo Block: 11413 chr10 18967678 20100781 1133104 5100 −0.232775998 0.755557369 hypo Block: 8805 chr10 1782851 3026903 1244053 11254 −0.211783865 0.761053162 hypo Block: 8707 chrX 103831927 105040920 1208994 3649 −0.217376256 0.660298472 hypo Block: 16204 chr2 5843401 6995750 1152350 8185 −0.22803249 0.742090721 hypo Block: 1489 chr3 173124980 174147410 1022431 4280 −0.256468744 0.726633598 hypo Block: 3605 chr12 99298164 100378195 1080032 4099 −0.242429985 0.702603798 hypo Block: 10666 chr13 34427720 35506342 1078623 5211 −0.24260414 0.775831088 hypo Block: 11032 chr5 17588719 18717318 1128600 4572 −0.229737539 0.730372689 hypo Block: 4540 chr4 175750609 176911745 1161137 4947 −0.223093606 0.740684266 hypo Block: 4399 chr17 31625297 32899372 1274076 8121 −0.20304692 0.673594472 hypo Block: 13205 chrX 75408913 76653463 1244551 3084 −0.206236156 0.676995693 hypo Block: 16123 chr8 49783393 50809666 1026274 4738 −0.249824224 0.723465401 hypo Block: 7517 chr4 16260058 17468256 1208199 6649 −0.21131939 0.734387295 hypo Block: 3884 chr13 72444367 73298256 853890 3699 −0.29894237 0.756284524 hypo Block: 11167 chr13 96751622 97580295 828674 3819 −0.306869912 0.74266103 hypo Block: 11228 chr7 136566655 137526888 960234 4743 −0.264784394 0.71882949 hypo Block: 7106 chr6 62179113 62986222 807110 2712 −0.314048354 0.755952587 hypo Block: 5810 chrX 136663678 137777263 1113586 3952 −0.227109008 0.677011104 hypo Block: 16324 chr7 83823355 84799327 975973 3594 −0.259063018 0.736909325 hypo Block: 6822 chr7 135665976 136544505 878530 3428 −0.286833974 0.717287089 hypo Block: 7104 chr3 73680359 74663468 983110 4457 −0.256160278 0.752777193 hypo Block: 3203 chr5 143585094 144711611 1126518 4044 −0.22335272 0.736403587 hypo Block: 5066 chr8 106335686 107276292 940607 3944 −0.267263178 0.748115525 hypo Block: 7761 chr4 30731414 31816116 1084703 4617 −0.231478943 0.765188282 hypo Block: 3919 chr2 180871900 181843440 971541 3505 −0.258430594 0.739437567 hypo Block: 2432 chr3 68057267 68973357 916091 3983 −0.273996436 0.72412874 hypo Block: 3175 chr3 55527657 56501406 973750 5508 −0.257260805 0.754646207 hypo Block: 3111 chr9 15601090 16726776 1125687 6817 −0.221468729 0.783145714 hypo Block: 7980 chr12 54982626 56039891 1057266 3957 −0.235781713 0.709892838 hypo Block: 10480 chr16 82675170 83841324 1166155 9030 −0.213596239 0.755351049 hypo Block: 12862 chr13 107571048 108512130 941083 5802 −0.264170673 0.720155401 hypo Block: 11294 chr22 34323251 35447616 1124366 5713 −0.21960069 0.713448838 hypo Block: 15633 chr3 34731284 35680458 949175 3336 −0.259793326 0.722094444 hypo Block: 2966 chr6 121762578 122715476 952899 3776 −0.258585201 0.715488464 hypo Block: 6037 chr4 111839127 113005446 1166320 4248 −0.211169788 0.70980457 hypo Block: 4196 chr10 112841466 113909773 1068308 5331 −0.230291455 0.723376242 hypo Block: 9325 chr2 209272057 210288391 1016335 3414 −0.241217458 0.711491672 hypo Block: 2567

TABLE 7 Partial list of small DMRs. Details, including column descriptions, are included in the Supplementary Methods. -Loss of boundary Mean Difference in Number of DMR Mean Normal Direction of Length Covered (Normal Methylation Methylation Type of small Chromosome Start End (bp) CpGs to Cancer) in DMR Change DMR Identifier # DMR chr16 51183143 51190667 7525 474 0.336 0.203 hyper SmallDMR: 8 other chr11 32454875 32461307 6433 400 0.343 0.131 hyper SmallDMR: 45 lossOfBoundary chr13 58203467 58209371 5905 379 0.371 0.297 hyper SmallDMR: 20 lossOfBoundary chr20 37351482 37358279 6798 434 0.316 0.187 hyper SmallDMR: 22 other chr8 54788861 54795497 6637 443 0.319 0.093 hyper SmallDMR: 7 boundaryShift chr20 55200051 55206547 6497 460 0.322 0.142 hyper SmallDMR: 6 boundaryShift chr13 53419184 53424656 5473 382 0.37 0.264 hyper SmallDMR: 16 boundaryShift chr10 7449233 7455383 6151 421 0.329 0.124 hyper SmallDMR: 1 lossOfBoundary chr3 44035725 44041323 5599 355 0.356 0.061 hyper SmallDMR: 2 lossOfBoundary chr8 10586790 10592484 5695 396 0.349 0.093 hyper SmallDMR: 15 lossOfBoundary chr16 54968642 54974174 5533 297 0.337 0.136 hyper SmallDMR: 252 lossOfBoundary chr7 49812207 49815938 3732 306 0.488 0.05 hyper SmallDMR: 3 lossOfBoundary chr6 166073666 166078543 4878 384 0.37 0.106 hyper SmallDMR: 5 boundaryShift chr13 112757596 112761523 3928 243 0.458 0.157 hyper SmallDMR: 46 lossOfBoundary chr13 28365972 28371719 5748 296 0.306 0.184 hyper SmallDMR: 259 other chr6 137813803 137819871 6069 320 0.277 0.154 hyper SmallDMR: 153 lossOfBoundary chr14 85995273 86001268 5996 338 0.276 0.157 hyper SmallDMR: 109 other chr11 79147781 79152750 4970 311 0.33 0.042 hyper SmallDMR: 25 lossOfBoundary chr6 166579057 166583822 4766 309 0.344 0.109 hyper SmallDMR: 64 lossOfBoundary chr9 135458625 135464563 5939 216 0.275 0.155 hyper SmallDMR: 1322 other chr6 73329426 73333491 4066 221 0.401 0.069 hyper SmallDMR: 47 boundaryShift chr16 67198985 67204158 5174 152 0.315 0.309 hyper SmallDMR: 1086 other chr13 88323452 88327174 3723 202 0.434 0.08 hyper SmallDMR: 135 boundaryShift chr6 163833773 163838195 4423 351 0.365 0.025 hyper SmallDMR: 10 other chr19 30015633 30020501 4869 376 0.324 0.144 hyper SmallDMR: 27 lossOfBoundary chr10 50816694 50822510 5817 385 0.269 0.223 hyper SmallDMR: 32 other chr9 100613916 100618137 4222 326 0.365 0.181 hyper SmallDMR: 49 lossOfBoundary chr1 217307316 217313506 6191 306 0.248 0.165 hyper SmallDMR: 152 lossOfBoundary chr6 390473 394427 3955 310 0.384 0.099 hyper SmallDMR: 4 lossOfBoundary chr13 102567686 102572645 4960 191 0.306 0.174 hyper SmallDMR: 196 other chr10 118030090 118034625 4536 305 0.331 0.104 hyper SmallDMR: 18 lossOfBoundary chr7 27182482 27186676 4195 215 0.357 0.45 hyper SmallDMR: 1563 boundaryShift chr7 98182674 98186076 3403 39 −0.44 0.709 hypo SmallDMR: 2562 other chr18 903631 909338 5708 339 0.262 0.174 hyper SmallDMR: 87 lossOfBoundary chr2 182544890 182549928 5039 250 0.296 0.136 hyper SmallDMR: 222 other chrX 113815462 113820414 4953 221 0.298 0.27 hyper SmallDMR: 501 boundaryShift chr5 37836119 37841020 4902 321 0.301 0.176 hyper SmallDMR: 40 lossOfBoundary chr11 69061244 69064318 3075 73 −0.477 0.837 hypo SmallDMR: 1491 boundaryShift chr6 127438642 127442978 4337 243 0.335 0.068 hyper SmallDMR: 23 boundaryShift chr20 23028137 23032338 4202 320 0.345 0.144 hyper SmallDMR: 13 lossOfBoundary chr8 145104341 145107516 3176 288 0.456 0.073 hyper SmallDMR: 26 boundaryShift chr7 155164119 155167895 3777 290 0.382 0.076 hyper SmallDMR: 77 boundaryShift chr13 95363007 95366074 3068 299 0.469 0.062 hyper SmallDMR: 30 other chr20 61048542 61052696 4155 290 0.337 0.18 hyper SmallDMR: 55 other chr10 57387143 57391537 4395 171 0.317 0.107 hyper SmallDMR: 326 lossOfBoundary chr20 61806468 61810902 4435 425 0.314 0.095 hyper SmallDMR: 9 other chr11 110581348 110584758 3411 221 0.407 0.041 hyper SmallDMR: 33 lossOfBoundary chr11 91956571 91960687 4117 258 0.335 0.072 hyper SmallDMR: 52 other chr13 93878699 93881494 2796 160 0.485 0.096 hyper SmallDMR: 138 other chr6 133561368 133565148 3781 209 0.358 0.083 hyper SmallDMR: 42 boundaryShift chr4 134067785 134073183 5399 302 0.25 0.155 hyper SmallDMR: 216 other chr6 94125909 94130589 4681 262 0.287 0.064 hyper SmallDMR: 41 lossOfBoundary chr20 61635973 61639232 3260 312 0.412 0.111 hyper SmallDMR: 53 other chr9 77111502 77116390 4889 243 0.273 0.087 hyper SmallDMR: 119 lossOfBoundary chr8 70981474 70985230 3757 284 0.354 0.138 hyper SmallDMR: 58 boundaryShift chr13 52529621 52533517 3897 57 −0.34 0.632 hypo SmallDMR: 2390 novelMethylation chr21 28215838 28219559 3722 247 0.355 0.042 hyper SmallDMR: 91 boundaryShift chr8 9760597 9765369 4773 279 0.271 0.11 hyper SmallDMR: 185 other chr8 72753797 72757389 3593 219 0.36 0.15 hyper SmallDMR: 225 lossOfBoundary chr13 110958465 110961303 2839 225 0.453 0.067 hyper SmallDMR: 36 lossOfBoundary chr10 106398343 106403103 4761 324 0.269 0.145 hyper SmallDMR: 24 lossOfBoundary chr13 84452863 84457882 5020 170 0.255 0.235 hyper SmallDMR: 387 other chr1 40150987 40156857 5871 42 −0.217 0.59 hypo SmallDMR: 10063 boundaryShift chr19 1465317 1468522 3206 330 0.397 0.197 hyper SmallDMR: 82 boundaryShift chr7 19155806 19159074 3269 218 0.388 0.104 hyper SmallDMR: 233 lossOfBoundary chr3 142837464 142840517 3054 296 0.414 0.086 hyper SmallDMR: 11 lossOfBoundary chr1 50880917 50884889 3973 247 0.318 0.122 hyper SmallDMR: 338 boundaryShift chr13 26623378 26626614 3237 238 0.39 0.127 hyper SmallDMR: 38 lossOfBoundary chr4 30721103 30725148 4046 338 0.311 0.121 hyper SmallDMR: 37 boundaryShift chr6 125282748 125285778 3031 172 0.413 0.056 hyper SmallDMR: 199 lossOfBoundary chr8 53850933 53854633 3701 262 0.337 0.137 hyper SmallDMR: 66 lossOfBoundary chr11 20180295 20185737 5443 260 0.228 0.177 hyper SmallDMR: 331 other chr20 59826523 59829497 2975 278 0.417 0.085 hyper SmallDMR: 14 lossOfBoundary chr10 134597791 134602559 4769 569 0.26 0.12 hyper SmallDMR: 17 lossOfBoundary chr2 1746207 1749394 3188 220 0.387 0.096 hyper SmallDMR: 59 lossOfBoundary chr13 73939583 73943635 4053 39 −0.303 0.652 hypo SmallDMR: 3146 other chr5 82766752 82770976 4225 201 0.289 0.044 hyper SmallDMR: 197 other chr9 101469049 101472291 3243 256 0.376 0.088 hyper SmallDMR: 19 lossOfBoundary chr2 115918267 115921372 3106 207 0.392 0.085 hyper SmallDMR: 48 lossOfBoundary chr6 6002294 6005227 2934 197 0.414 0.124 hyper SmallDMR: 549 other chr17 1959436 1962815 3380 333 0.359 0.109 hyper SmallDMR: 137 boundaryShift chr2 5830537 5834912 4376 324 0.277 0.221 hyper SmallDMR: 61 lossOfBoundary chr2 193058020 193061739 3720 190 0.324 0.101 hyper SmallDMR: 166 lossOfBoundary chr2 119913025 119916999 3975 272 0.303 0.164 hyper SmallDMR: 114 boundaryShift chr10 129533359 129537556 4198 279 0.284 0.22 hyper SmallDMR: 157 boundaryShift chr12 111470562 111474977 4416 272 0.263 0.089 hyper SmallDMR: 69 lossOfBoundary chr16 56224046 56228744 4699 252 0.247 0.096 hyper SmallDMR: 96 other chr7 136552959 136556557 3599 191 0.321 0.209 hyper SmallDMR: 398 other chr16 86598833 86602750 3918 324 0.294 0.15 hyper SmallDMR: 122 other chr8 77593058 77596382 3325 146 0.346 0.111 hyper SmallDMR: 702 other chr2 213400355 213404526 4172 228 0.275 0.087 hyper SmallDMR: 117 lossOfBoundary chr20 54577883 54581285 3403 213 0.335 0.261 hyper SmallDMR: 200 lossOfBoundary chr1 119548395 119551319 2925 199 0.389 0.122 hyper SmallDMR: 330 other chr2 154727485 154730720 3236 146 0.351 0.178 hyper SmallDMR: 267 lossOfBoundary chr7 15724433 15728177 3745 154 0.302 0.111 hyper SmallDMR: 382 boundaryShift chr3 192125431 192128625 3195 208 0.353 0.105 hyper SmallDMR: 70 lossOfBoundary chr7 155255369 155259176 3808 98 0.295 0.2 hyper SmallDMR: 3031 other chr1 114694766 114698574 3809 244 0.294 0.13 hyper SmallDMR: 54 lossOfBoundary chr13 109147076 109149637 2562 151 0.435 0.183 hyper SmallDMR: 167 lossOfBoundary chr16 69105495 69108076 2582 24 −0.431 0.815 hypo SmallDMR: 3410 novelMethylation chr1 57887008 57890941 3934 231 0.282 0.104 hyper SmallDMR: 192 lossOfBoundary chr8 128752277 128754623 2347 37 −0.47 0.769 hypo SmallDMR: 2746 other chr3 184628231 184630670 2440 26 −0.451 0.806 hypo SmallDMR: 3211 novelMethylation chr3 6901652 6905259 3608 170 0.304 0.178 hyper SmallDMR: 414 lossOfBoundary chr2 239754875 239758481 3607 317 0.304 0.165 hyper SmallDMR: 28 lossOfBoundary chr13 37004036 37007372 3337 186 0.326 0.241 hyper SmallDMR: 187 lossOfBoundary chr10 125851090 125854029 2940 252 0.37 0.054 hyper SmallDMR: 60 boundaryShift chr11 17740109 17743884 3776 271 0.287 0.178 hyper SmallDMR: 94 lossOfBoundary chr10 83633120 83636930 3811 245 0.284 0.14 hyper SmallDMR: 86 other chr5 127871927 127875163 3237 218 0.334 0.189 hyper SmallDMR: 72 lossOfBoundary chr20 25063432 25065910 2479 142 0.436 0.166 hyper SmallDMR: 911 other chr7 24322944 24325427 2484 150 0.435 0.149 hyper SmallDMR: 274 lossOfBoundary chr13 35514882 35518317 3436 156 0.314 0.053 hyper SmallDMR: 143 lossOfBoundary chr11 20690107 20693192 3086 180 0.348 0.102 hyper SmallDMR: 150 other chr8 132051575 132055090 3516 253 0.304 0.239 hyper SmallDMR: 83 lossOfBoundary chr8 72468356 72471549 3194 166 0.334 0.117 hyper SmallDMR: 742 lossOfBoundary chr7 3339234 3342464 3231 247 0.33 0.065 hyper SmallDMR: 21 boundaryShift chr2 235933204 235936653 3450 91 −0.308 0.651 hypo SmallDMR: 1770 novelMethylation chr20 24449386 24452209 2824 216 0.376 0.081 hyper SmallDMR: 35 lossOfBoundary chr10 28033400 28036407 3008 213 0.351 0.097 hyper SmallDMR: 193 other chr8 85094124 85097366 3243 150 0.325 0.13 hyper SmallDMR: 510 boundaryShift chr12 24714149 24717242 3094 165 0.34 0.041 hyper SmallDMR: 145 other chr11 27739449 27744983 5535 248 0.19 0.118 hyper SmallDMR: 133 other chr22 26062312 26065156 2845 27 −0.369 0.753 hypo SmallDMR: 3690 other chr1 34628535 34632537 4003 244 0.262 0.064 hyper SmallDMR: 162 boundaryShift chr8 65281163 65284678 3516 189 0.298 0.189 hyper SmallDMR: 484 other chr8 24812925 24816381 3457 206 0.303 0.09 hyper SmallDMR: 215 other chr20 50720243 50722807 2565 159 0.408 0.098 hyper SmallDMR: 565 lossOfBoundary chr18 5544506 5548672 4167 25 −0.251 0.711 hypo SmallDMR: 10088 other chr6 10881682 10884891 3210 123 0.324 0.255 hyper SmallDMR: 954 other chr10 100991745 100996944 5200 219 0.2 0.177 hyper SmallDMR: 270 boundaryShift chr11 128562106 128565519 3414 217 0.303 0.083 hyper SmallDMR: 211 other chr3 128210180 128212550 2371 175 0.435 0.115 hyper SmallDMR: 658 other chr13 39260101 39262646 2546 144 0.405 0.096 hyper SmallDMR: 130 boundaryShift chr18 25754857 25758958 4102 290 0.251 0.061 hyper SmallDMR: 113 lossOfBoundary chr12 72664965 72668243 3279 220 0.313 0.143 hyper SmallDMR: 169 lossOfBoundary chr4 62065454 62069488 4035 260 0.254 0.129 hyper SmallDMR: 120 lossOfBoundary chr6 118227570 118230205 2636 217 0.388 0.063 hyper SmallDMR: 31 lossOfBoundary chr8 140714169 140718258 4090 294 0.25 0.103 hyper SmallDMR: 65 other chr7 157476522 157478768 2247 197 0.455 0.126 hyper SmallDMR: 262 other

TABLE 8 Genomic features of Differentially Methylated Regions (DMRs) in colon cancer. Median size Overlap with Overlap with Overlap with Refseq N # CpG Genomic size (bp) islands shores mRNA TSS Normal genome (reference) N/A  28.2M 3.10 Gb N/A 27.7K 55.4K 36,983 Hypomethylated blocks 13,540  16.2M 1.95 Gb 39,412 17.6% 26.8% 10,453 Hypermethylated blocks 2,871 485K 35.8 Mb 9,213 13.4% 36.4% 976 Hypomethylated small DMRs 4,315  59.5K 2.91 Mb 401 2.2% 51.0% 1,708 Novel hypomethylated 448  8.35K  367 Kb 658 2.9% 19.9% 30 Shift of methylation boundary 1,516  17.5K  741 Kb 261 2.1% 92.8% 1,313 Hypermethylated small DMRs 5,810 403K 6.14 Mb 820 67.2% 17.0% 3,068 Loss of boundary* 1,756 165K 2.36 Mb 1,159 80.9% 3.4% 1,091 Shift of methylation boundary 1,774  96.3K 1.40 Mb 502 60.3% 33.0% 1,027 *As described in the text, loss of boundary DMRs were associated with increase of methylation in the CpG island and a decrease of methylation in the adjacent shore. These were scored as a single event and classify them here since there are more CpGs in the islands than in the shores.

TABLE 9 The overlap of various genomic domains with differentially methylated regions in colon cancer. Size (in Overlap Overlap with Genomic Size millions with blocks blocks (in Odds domain (in GB) of CpGs) (in GB) millions of CpGs) Ratio Repeats 1.45 14.8 1.04 GB 9.33 1.4 PMDs 1.23 10.0 1.14 GB 8.45 6.5 LOCKs 0.77 5.8 697 MB 5.06 6.8 LADs 1.14 8.6 989 MB 7.10 4.9 The size of genomic domains are shown in column 1 in gigabases and column 2 in number of CpGs. Column 3 shows the overlap in gigabases and Column 4 in number of CpGs. Column 5 shows the observed to expected by chance odds ratio. All the overlaps were statistically significant (p < 2.2 × 10~¹⁶).

TABLE 10 Enrichment of hypervariably methylated loci identified by the custom Illumina array in blocks identified by bisulfite sequencing. Hypervariable CpGs in all tissue types (custom array) Non-variably methylated Hypo- Hyper- CpGs in colon cancer methylated methylated (Illumina 27k) Number of CpGs 81 52 16,049 Inside 63%  4% 13% Hypomethylated Blocks Inside  5% 37%  2% Hypermethylated Blocks

TABLE 11 Methylation values* observed in CpG islands in cancer compared to normal samples. No Methylation status in normals Total Hypo change Hyper Unmethylated (<=0.2) 16184 0.1% 83.2% 16.7% Partial methylated (>=0.2, <=0.8) 4796 17.0% 46.7% 36.3% Methylated (>=0.8) 5527 24.0% 75.9% 0.1% *Average methylation value in each island were then averaged across subject for cancer and normal samples separately

TABLE 12 Gene expression negatively correlates with methylation in small DMRs. Associated Inversely Percent Inverse Genes correlated genes correlated Shift of boundary 2,273 1,192 52% (hypomethylated) Novel hypomethylation 38 17 45% Other hypomethylated 442 192 43% Shift of boundary 1,893 532 30% (hypermethylation) Loss of regulation 1,119 346 31% (hypermethylation) Other hypermethylated 1,204 335 28% Each gene represented in a microarray experiment was mapped to the closest small DMR, with a gene and a DMR considered associated if the DMR was within 2 kbp from the transcription start site of the gene; 6,869 genes were mapped and are represented in the table. For each of the small DMR classes, as defined in main text, the number of associated genes that were differentially expressed (FDR < 0.05) and had an inverse relationship was computed.

TABLE 13 Gene ontology enrichment analysis of differentially expressed genes associated with hypomethyiated boundary shifts. Expected Odds Gene ontology term count Count Size ratio P-value Q-value Mitotic cell cycle 11.6 31 185 3.1 3.8 × 10′″ 0.00036 Cell cycle process 18.7 42 297 2.6 5.4 × 10′″ 0.00036 Mitosis 9.9 25 157 2.9 1.5 × 10* 0.006 Positive regulation of ubiquitin-protein 3.9 14 61 4.5 2.0 × 10″⁵ 0.0071 ligase activity during mitotic cell cycle Organelle fission 13.7 30 216 2.5 3.6 × 10″^(b) 0.0097 The differentially expressed genes comparing colon cancer samples to normal samples were divided into two groups: those associated hypomethyiated boundary shifts and the rest. The table shows the five categories with statistically significant enrichment (FDRO.01).

TABLE 14 List of genes showing statistically significant over-expression in cancer compared to normal samples and are within 2,000 bp from an outward methylation boundary shift. geneName methDiff diffExp qvalue chr strand txStart txEnd QPCT −0.287228151 2.75440168 1.28E−19 chr2 1 37571717 37600465 ANLN −0.386314449 2.412402373 3.29E−13 chr7 1 36429415 36493400 SLC6A6 −0.277217014 2.372018352 2.61E−17 chr3 1 14444076 14530857 CEP55 −0.401964569 2.249352145 7.03E−14 chr10 1 95256389 95288849 ANLN −0.386314449 2.121207986 5.50E−14 chr7 1 36429415 36493400 TGFBI −0.387333797 2.083655423 2.69E−17 chr5 1 135364584 135399506 ME1 −0.239140622 2.064347685 1.07E−11 chr6 −1 83920108 84140790 TRIP13 −0.391690922 1.852594706 3.17E−18 chr5 1 892758 918235 CTPS −0.283453124 1.845547869 7.21E−17 chr1 1 41445007 41478235 ME1 −0.239140622 1.836087668 6.29E−13 chr6 −1 83920108 84140790 HELLS −0.481250286 1.786723981 7.81E−16 chr10 1 96305574 96361856 CCNB1 −0.344279127 1.720916748 5.09E−10 chr5 1 68462837 68474072 MET −0.464402149 1.713620728 2.19E−25 chr7 1 116312446 116438440 TRIP6 −0.311643639 1.612698985 9.99E−19 chr7 1 100464760 100471076 −0.265818173 1.584054427 3.42E−09 chr6 1 31913486 31919861 IL20RA −0.326941415 1.574006752 5.92E−13 chr6 −1 137321108 137366101 TTK −0.365969645 1.554795792 5.04E−10 chr6 1 80714322 80752244 CDK1 −0.349676581 1.554401898 2.32E−16 chr10 1 62538212 62554610 PRC1 −0.278283026 1.553574908 3.00E−14 chr15 −1 91509275 91537749 CCNB1 −0.344279127 1.550393107 8.02E−14 chr5 1 68462837 68474072 CDCA2 −0.264275049 1.548451703 1.88E−12 chr8 1 25316513 25365436 ARG2 −0.353923274 1.539462883 8.15E−10 chr14 1 68086579 68118437 PHF19 −0.410901232 1.504592686 1.06E−17 chr9 −1 123617977 123639606 SLC6A6 −0.277217014 1.467899072 4.24E−13 chr3 1 14444076 14530857 TK1 −0.225975437 1.465582264 1.35E−16 chr17 −1 76170160 76183314 CDK1 −0.349676581 1.462604059 1.32E−12 chr10 1 62538212 62554610 C12orf48 −0.315593006 1.454752076 3.05E−11 chr12 1 102513956 102591298 LRRC6 −0.254379418 1.438052039 3.03E−19 chr8 −1 133584449 133687813 CDKN3 −0.296939585 1.437015156 1.43E−12 chr14 1 54863673 54886936 MET −0.464402149 1.432662311 1.03E−12 chr7 1 116312446 116438440 CDKN3 −0.296939585 1.426456138 3.41E−13 chr14 1 54863673 54886936 ITGA2 −0.273672477 1.424782914 1.79E−16 chr5 1 52285156 52390609 GART −0.265804362 1.422971299 4.70E−12 chr21 −1 34876238 34915148 KPNA2 −0.325507566 1.420135526 7.43E−16 chr17 1 66031848 66042969 MET −0.464402149 1.409380516 1.96E−13 chr7 1 116312446 116438440 FAM57A −0.258171163 1.405422919 7.77E−14 chr17 1 635798 646074 CDK1 −0.349676581 1.404039029 1.58E−11 chr10 1 62538212 62554610 GPT2 −0.302235264 1.397275797 9.65E−14 chr16 1 46918290 46965201 PDCD2L −0.244419742 1.395394063 2.78E−20 chr19 1 34895303 34917070 C12orf48 −0.315593006 1.384890241 6.99E−12 chr12 1 102513956 102591298 SLC39A10 −0.242261524 1.362347636 1.03E−12 chr2 1 196521471 196602426 HOXB6 −0.391990817 1.360310033 7.76E−08 chr17 −1 46673114 46682354 MET −0.464402149 1.353903556 7.36E−14 chr7 1 116312446 116438440 DHFRP1 −0.33197287 1.333474721 1.13E−11 chr5 −1 79922047 79950802 −0.33891476 1.309093323 1.48E−17 chr2 1 173940442 174131511 ERO1L −0.337054537 1.300900638 9.09E−13 chr14 −1 53106634 53162423 FERMT1 −0.270407533 1.292003455 1.24E−19 chr20 −1 6055492 6104191 MOCOS −0.26317804 1.285728037 3.95E−07 chr18 1 33767482 33852120 GART −0.265804362 1.265297033 1.52E−16 chr21 −1 34876238 34915148 FERMT1 −0.270407533 1.258010636 5.17E−18 chr20 −1 6055492 6104191 C1orf59 −0.269034512 1.256263577 3.98E−15 chr1 −1 109190917 109204148 CENPH −0.258617525 1.255179781 4.77E−11 chr5 1 68485375 68506184 RUVBL1 −0.261371583 1.250774746 3.25E−18 chr3 −1 127799803 127842667 FBXO5 −0.274244427 1.250044053 6.75E−10 chr6 −1 153291664 153304153 SPNS2 −0.26292891 1.24910284 2.34E−15 chr17 1 4402129 4443228 SLC22A3 −0.419938177 1.232083732 1.63E−08 chr6 1 160769300 160873613 SCD −0.412561336 1.23021566 9.78E−06 chr10 1 102106877 102116367 C13orf37 −0.282975063 1.227299642 1.53E−13 chr13 −1 73282495 73301825 TK1 −0.225975437 1.215067193 9.23E−16 chr17 −1 76170160 76183314 ODC1 −0.42700535 1.211699492 2.39E−14 chr2 −1 10580094 10588630 PLK4 −0.310709849 1.195732188 1.21E−10 chr4 1 128802016 128820350 BYSL −0.306448506 1.193699275 1.33E−19 chr6 1 41888926 41900784 ASPM −0.315933748 1.185003139 4.09E−08 chr1 −1 197053258 197115824 FERMT1 −0.270407533 1.158992882 2.40E−15 chr20 −1 6055492 6104191 GMDS −0.299511508 1.156279571 9.93E−16 chr6 −1 1624041 2245915 SHMT2 −0.240887472 1.152051089 3.60E−14 chr12 1 57623519 57628509 C7orf68 −0.427832848 1.152003901 2.58E−18 chr7 1 128095903 128097978 C7orf68 −0.427832848 1.137362258 1.25E−19 chr7 1 128095903 128097978 GMDS −0.299511508 1.123033393 9.02E−18 chr6 −1 1624041 2245915 TIMELESS −0.30942338 1.118520353 2.14E−14 chr12 −1 56810158 56843200 KPNA2 −0.325507566 1.114430687 5.01E−14 chr17 1 66031848 66042969 RAB23 −0.340951531 1.100310587 1.56E−09 chr6 −1 57054597 57086205 AURKA −0.293961713 1.099330524 1.24E−11 chr20 −1 54944446 54967261 TACC3 −0.267804701 1.087928887 1.23E−12 chr4 1 1723266 1746898 SQLE −0.412483745 1.08596534 7.33E−07 chr8 1 126010720 126034525 NUP37 −0.315593006 1.085282612 2.67E−17 chr12 −1 102467975 102512361 CTHRC1 −0.324284535 1.081056474 3.24E−05 chr8 1 104383743 104395221 RTEL1 −0.24942297 1.069116794 9.01E−08 chr20 1 62290756 62330051 NUFIP1 −0.272420763 1.068531277 6.09E−16 chr13 −1 45513384 45563618 PLK1 −0.269395632 1.065948279 3.60E−11 chr16 1 23690143 23701688 C12orf29 −0.327535911 1.064878076 6.83E−10 chr12 1 88429290 88443935 CEP76 −0.224568396 1.054054095 1.44E−07 chr18 −1 12672631 12702773 DTYMK −0.259366156 1.052061774 6.56E−17 chr2 −1 242615157 242626406 PHF19 −0.410901232 1.042169399 4.29E−17 chr9 −1 123631865 123639466 RAD18 −0.294092376 1.040826053 2.11E−07 chr3 −1 8918760 9005186 SCD −0.412561336 1.040246085 5.54E−06 chr10 1 102106881 102124591 RAB23 −0.340951531 1.029194137 4.06E−11 chr6 −1 57053607 57087078 YAP1 −0.260585002 1.02763996 4.63E−09 chr11 1 101981210 102104154 GSTP1 −0.335937288 1.024251451 6.99E−17 chr11 1 67351066 67354131 NOLC1 −0.384383152 1.020987106 5.90E−14 chr10 1 103912117 103923623 DTYMK −0.259366156 1.012686833 2.20E−15 chr2 −1 242615157 242626406 PLEK2 −0.320540707 1.006985665 6.83E−14 chr14 −1 67853702 67878828 SHMT2 −0.240887472 1.006656875 2.45E−17 chr12 1 57623519 57628509 CEP76 −0.224568396 1.004572951 1.07E−10 chr18 −1 12672631 12702773 PLK4 −0.310709849 1.002496079 8.78E−08 chr4 1 128802016 128820350 JAG1 −0.207653553 0.998751445 3.94E−10 chr20 −1 10618332 10654608 PKM2 −0.26154852 0.991259837 1.30E−11 chr15 −1 72491373 72523328 NKD1 −0.323367141 0.990807307 9.53E−10 chr16 1 50582241 50670647 AURKA −0.293961713 0.990673621 5.51E−11 chr20 −1 54944446 54967261 FGGY −0.275459464 0.990581427 5.38E−13 chr1 1 59762663 60228402 SHMT2 −0.240887472 0.989026812 6.19E−14 chr12 1 57623519 57628509 FBXO22OS −0.249605837 0.987940737 4.95E−15 chr15 1 76196200 76227609 SNORD118 −0.269386914 0.983977501 4.91E−07 chr17 −1 8076296 8079714 DPCD −0.218924523 0.982360775 7.55E−14 chr10 1 103348045 103369425 AHCY −0.273213996 0.980581533 1.87E−18 chr20 −1 32868074 32891154 FZD6 −0.265219075 0.978554009 1.15E−11 chr8 1 104311100 104345087 CDCA2 −0.264275049 0.977693264 1.32E−11 chr8 1 25316513 25365436 WARS2 −0.214976156 0.974056434 1.76E−11 chr1 −1 119573839 119683271 MTHFD2 −0.43988327 0.971127387 2.68E−13 chr2 1 74425689 74444692 PGM2L1 −0.340496727 0.965882382 8.09E−11 chr11 −1 74041361 74109502 WDHD1 −0.221635494 0.960208966 4.74E−10 chr14 −1 55405668 55493795 FHL2 −0.370777923 0.949510686 6.20E−11 chr2 −1 105974169 106016124 PGM2L1 −0.340496727 0.940564013 1.46E−08 chr11 −1 74041361 74109502 FBXO5 −0.274244427 0.935975694 5.50E−10 chr6 −1 153291664 153304153 SQLE −0.412483745 0.934244029 3.81E−07 chr8 1 126010720 126034525 IL20RA −0.326941415 0.931939035 1.39E−14 chr6 −1 137321108 137366101 FASN −0.307722725 0.924131378 5.66E−11 chr17 −1 80036215 80056106 ABHD2 −0.335157092 0.920873632 3.46E−05 chr15 1 89631405 89745591 KIAA1704 −0.272420763 0.918447128 5.26E−10 chr13 1 45563687 45602405 GART −0.265804362 0.918196342 1.56E−15 chr21 −1 34876238 34915148 NOLC1 −0.384383152 0.914043684 1.03E−14 chr10 1 103912117 103923623 FBXO22OS −0.249605837 0.909039543 1.93E−10 chr15 1 76196200 76227609 −0.33891476 0.907054142 9.74E−06 chr2 1 173940570 174091874 VANGL1 −0.35350898 0.906722654 1.11E−09 chr1 1 116184612 116236312 IMMP2L −0.34514707 0.905774603 6.28E−17 chr7 −1 110303110 111202347 NKD1 −0.323367141 0.905103602 9.77E−08 chr16 1 50582241 50670647 ZYX −0.307434113 0.902904178 9.58E−11 chr7 1 143078173 143088204 ABHD2 −0.335157092 0.900969804 3.31E−07 chr15 1 89631405 89745591 FBXO22OS −0.249605837 0.900721794 1.66E−09 chr15 1 76196200 76227609 ENAH −0.297371742 0.899092283 9.76E−15 chr1 −1 225680538 225840844 INCENP −0.296869408 0.896357006 9.14E−06 chr11 1 61891445 61920635 LACTB2 −0.399766137 0.894630027 2.34E−09 chr8 −1 71549501 71581447 ALDH7A1 −0.296044325 0.891523928 7.01E−13 chr5 −1 125877533 125931110 ITGA2 −0.273672477 0.889972605 3.79E−14 chr5 1 52285156 52390609 SCD −0.412561336 0.881962999 3.65E−05 chr10 1 102106881 102124591 DHFRP1 −0.33197287 0.881776578 8.37E−11 chr5 −1 79922047 79950802 BAX −0.426714351 0.880411505 6.30E−07 chr19 1 49458134 49465055 LACTB2 −0.399766137 0.875181214 5.88E−05 chr8 −1 71549501 71581447 MRPS17 −0.389012137 0.873580896 2.82E−14 chr7 1 56019512 56024192 ENO1 −0.319058202 0.872725187 1.15E−10 chr1 −1 8921061 8938749 C12orf5 −0.380595644 0.872649011 1.95E−07 chr12 1 4430359 4469188 ERCC8 −0.28157772 0.870429148 1.91E−06 chr5 −1 60169659 60240878 PGD −0.241805413 0.864482413 4.20E−13 chr1 1 10459137 10480201 IPO7 −0.428150813 0.862597647 1.00E−17 chr11 1 9406169 9469673 RPP25 −0.361427208 0.858972588 2.49E−08 chr15 −1 75247443 75249775 NUP35 −0.392937687 0.858359924 2.99E−09 chr2 1 183989083 184026408 FAM175A −0.267694635 0.85802511 8.44E−06 chr4 −1 84382092 84406334 PHLDA2 −0.34276695 0.857310418 1.42E−07 chr11 −1 2949503 2950685 MEST −0.306641166 0.856733533 1.71E−13 chr7 1 130126046 130146133 NOP58 −0.431871435 0.855922392 2.94E−16 chr2 1 203130439 203168389 GLRX3 −0.468137547 0.855536417 4.57E−14 chr10 1 131934663 131977888 C1orf135 −0.251930519 0.854987468 2.00E−11 chr1 −1 26160497 26185903 C17orf75 −0.282147578 0.853046303 1.95E−09 chr17 −1 30658392 30669189 IPO7 −0.428150813 0.85180088 3.80E−17 chr11 1 9406169 9469673 XPO5 −0.290308924 0.85027956 1.62E−14 chr6 −1 43490072 43543812 YAP1 −0.260585002 0.8470295 3.52E−11 chr11 1 101981210 102104154 WARS2 −0.214976156 0.845887997 5.42E−06 chr1 −1 119573839 119683271 DUS4L −0.239778252 0.845173583 1.74E−11 chr7 1 107204403 107218906 ERO1L −0.337054537 0.844206961 2.66E−08 chr14 −1 53106634 53162423 NANP −0.265582678 0.841562243 6.12E−13 chr20 −1 25593571 25604811 DNAJC2 −0.335527424 0.840151967 5.99E−15 chr7 −1 102952921 102985113 XPO5 −0.290308924 0.838685895 2.55E−15 chr6 −1 43490072 43543812 NOLC1 −0.384383152 0.838656605 1.11E−12 chr10 1 103912117 103923623 PPAP2C −0.241595108 0.838211159 1.56E−10 chr19 −1 281048 291435 HSPD1 −0.365274716 0.829443889 2.30E−13 chr2 −1 198351305 198364771 −0.33891476 0.829083868 2.87E−06 chr2 1 173940570 174091874 EPT1 −0.286072226 0.828758101 3.04E−06 chr2 1 26568982 26618759 C14orf126 −0.429259277 0.824406285 5.07E−05 chr14 −1 31915242 31926670 GNPNAT1 −0.412868705 0.822945344 1.59E−14 chr14 −1 53241912 53258319 PDXK −0.451405538 0.821714738 2.26E−13 chr21 1 45138978 45182188 EPHA1 −0.279704626 0.820944361 1.01E−12 chr7 −1 143088205 143105985 −0.33891476 0.819965659 1.20E−06 chr2 1 173940570 174091874 L2HGDH −0.234782015 0.818880596 1.55E−10 chr14 −1 50712120 50778947 PTPLAD1 −0.27257057 0.816192599 5.85E−09 chr15 1 65822825 65870693 TOMM34 −0.299060249 0.814773814 1.83E−19 chr20 −1 43570771 43589127 CTSH −0.301656861 0.813029733 2.03E−06 chr15 −1 79213400 79237433 PUS1 −0.291126169 0.812913155 2.32E−11 chr12 1 132413813 132428404 RSL1D1 −0.31776943 0.809676853 1.51E−16 chr16 −1 11931196 11945442 TBC1D7 −0.327292622 0.805149062 6.80E−11 chr6 −1 13305183 13328763 TIMM50 −0.263467531 0.800544699 1.21E−15 chr19 1 39971052 39981528 MCFD2 −0.291486921 0.800187491 8.42E−10 chr2 −1 47129013 47143007 DNAJC9 −0.362712454 0.79566698 1.29E−12 chr10 −1 75002582 75008620 TBRG4 −0.352890468 0.791795428 6.00E−19 chr7 −1 45139699 45151317 ALDH7A1 −0.296044325 0.79032756 8.34E−11 chr5 −1 125877533 125931110 GCSH −0.453192502 0.787464518 9.88E−14 chr16 −1 81115566 81130008 CAMSAP1 −0.232304633 0.785972505 1.87E−07 chr9 −1 138700333 138799070 JAG1 −0.207653553 0.785933601 4.58E−10 chr20 −1 10618332 10654608 CDK7 −0.34382059 0.783249994 5.44E−13 chr5 1 68530700 68573250 NSUN4 −0.390831198 0.778904391 1.25E−13 chr1 1 46805849 46827863 IPO7 −0.428150813 0.775002569 4.64E−15 chr11 1 9406169 9469673 TROAP −0.329360048 0.770726977 3.08E−13 chr12 1 49716971 49725514 ZMYND19 −0.276199921 0.770129623 2.80E−13 chr9 −1 140476531 140484942 C1orf135 −0.251930519 0.768989781 7.16E−11 chr1 −1 26160497 26185903 GEMIN5 −0.309935801 0.768826256 7.49E−11 chr5 −1 154266976 154317769 MKLN1 −0.285004864 0.762718997 2.22E−09 chr7 1 131012619 131181395 SHB −0.337673042 0.760275993 1.17E−08 chr9 −1 37919131 38069208 SKA2 −0.223170945 0.757405762 1.35E−05 chr17 −1 57187308 57232800 TNFRSF10A −0.384420552 0.757083317 9.22E−06 chr8 −1 23048064 23082639 CKLF −0.238225994 0.756641822 1.88E−11 chr16 1 66586470 66599975 CKS1B −0.255490761 0.756314088 3.28E−11 chr1 1 154947159 154951160 NDUFAF2 −0.28157772 0.756215701 1.06E−14 chr5 1 60240956 60448853 PTPLAD1 −0.27257057 0.754993736 1.07E−13 chr15 1 65822825 65870693 PDXK −0.451405538 0.753333567 3.50E−10 chr21 1 45138978 45182188 RFWD3 −0.300370479 0.751685588 1.36E−09 chr16 −1 74655297 74700779 ZC3H8 −0.269560486 0.749208926 1.40E−10 chr2 −1 112973254 113012688 NUBPL −0.389729092 0.748925872 6.70E−09 chr14 1 32030591 32330399 ENAH −0.297371742 0.747939499 1.99E−09 chr1 −1 225680538 225840844 DDX56 −0.233165466 0.746717992 7.36E−15 chr7 −1 44605016 44613601 VANGL1 −0.35350898 0.746078634 6.34E−13 chr1 1 116184612 116236312 UCHL3 −0.298552217 0.744844024 5.16E−16 chr13 1 76123927 76180069 ICA1 −0.256836172 0.74182404 2.25E−11 chr7 −1 8152814 8301911 C5orf34 −0.339621872 0.740748574 1.74E−10 chr5 −1 43486803 43515247 POLH −0.290308924 0.737584811 4.09E−09 chr6 1 43543887 43583397 JAG1 −0.207653553 0.736825006 8.03E−10 chr20 −1 10618332 10654608 IPO7 −0.428150813 0.73656029 1.19E−11 chr11 1 9406169 9469673 ACP1 −0.243372223 0.736343968 4.11E−10 chr2 1 264872 278283 CCT4 −0.378022827 0.733078592 1.79E−16 chr2 −1 62095224 62115939 WEE1 −0.307311914 0.73299823 2.85E−08 chr11 1 9595430 9611531 HIBADH −0.435762995 0.732515757 2.30E−08 chr7 −1 27565061 27702614 YAP1 −0.260585002 0.72843054 2.88E−12 chr11 1 101981210 102104154 DHFRP1 −0.33197287 0.727823904 2.32E−10 chr5 −1 79922047 79950802 FAM161A −0.256344752 0.727276263 3.08E−07 chr2 −1 62051991 62081278 EXOC6 −0.394254414 0.727205205 2.92E−08 chr10 1 94608277 94819247 NUFIP1 −0.272420763 0.724642728 1.47E−10 chr13 −1 45513384 45563618 PTPLAD1 −0.27257057 0.72301388 1.88E−13 chr15 1 65822825 65870693 ST7OT3 −0.478497425 0.722972073 1.81E−10 chr7 1 116593396 116870157 GART −0.265804362 0.722463568 3.05E−06 chr21 −1 34896316 34914420 GTF3C3 −0.354411257 0.720907079 9.26E−11 chr2 −1 197627756 197664425 FAM128A −0.245234229 0.720094937 3.73E−14 chr2 −1 132241533 132249995 ICA1 −0.256836172 0.719314832 1.84E−10 chr7 −1 8152814 8301911 BAX −0.426714351 0.717540312 2.04E−06 chr19 1 49458134 49465055 ENO1 −0.319058202 0.716641772 2.86E−14 chr1 −1 8921061 8938749 SUSD1 −0.322450196 0.715526839 2.46E−12 chr9 −1 114803065 114937465 SKIL −0.332370272 0.715182799 0.000149056 chr3 1 170077411 170111651 SLC6A6 −0.277217014 0.714295976 2.30E−08 chr3 1 14444076 14530857 UBE3C −0.265141265 0.714147489 1.31E−05 chr7 1 156931607 157062066 MTHFD2 −0.43988327 0.713674028 1.51E−08 chr2 1 74425689 74444692 METTL5 −0.344642797 0.711769057 1.99E−15 chr2 −1 170668267 170681424 C7orf44 −0.31688192 0.710412079 1.24E−09 chr7 −1 43678856 43769088 NAA38 −0.28832537 0.70683953 1.44E−10 chr7 1 117824086 117832878 PSMDI2 −0.248429065 0.706839498 2.82E−11 chr17 −1 65334032 65362743 UBA2 −0.333463383 0.704795848 9.21E−17 chr19 1 34919268 34960795 INTS2 −0.31571998 0.703832765 6.97E−08 chr17 −1 59942735 60005377 SCD −0.412561336 0.701871865 1.04E−05 chr10 1 102106881 102124591 ZYX −0.307434113 0.701046775 1.48E−09 chr7 1 143078173 143088204 C12orf45 −0.340238462 0.700170696 7.29E−13 chr12 1 105380098 105388505 PHF19 −0.410901232 0.699152416 1.46E−15 chr9 −1 123617977 123639606 PTPLAD1 −0.27257057 0.693142858 2.79E−16 chr15 1 65822825 65870693 CCT8 −0.286031759 0.69055968 8.33E−15 chr21 −1 30428645 30446118 GTPBP10 −0.279762111 0.689791718 9.64E−10 chr7 1 89975979 90015204 POLR3K −0.216414146 0.686340216 8.08E−12 chr16 −1 96407 103628 ZNF200 −0.352071153 0.685460602 7.58E−07 chr16 −1 3272325 3285175 DCLRE1A −0.273346942 0.683924106 2.36E−11 chr10 −1 115594488 115614142 CSTF3 −0.245463178 0.683219717 5.67E−05 chr11 −1 33106137 33183037 CKLF −0.238225994 0.682582084 3.39E−09 chr16 1 66586470 66599975 MAP3K8 −0.28698722 0.682293632 6.32E−06 chr10 1 30722866 30750762 C12orf29 −0.327535911 0.679763512 1.21E−07 chr12 1 88429290 88443935 POLR1D −0.338281428 0.677608966 1.64E−14 chr13 1 28194903 28197589 −0.33891476 0.676454786 5.43E−09 chr2 1 173940687 174132738 C14orf126 −0.429259277 0.676041167 2.66E−08 chr14 −1 31915242 31926670 DHFRP1 −0.33197287 0.675947124 8.21E−07 chr5 −1 79922047 79950802 CCT5 −0.247574331 0.674240944 6.29E−13 chr5 1 10250033 10266524 POLH −0.290308924 0.671436242 8.55E−10 chr6 1 43543887 43583397 FPGS −0.280832452 0.670652282 3.18E−14 chr9 1 130565154 130576343 GCSH −0.453192502 0.668277808 3.59E−11 chr16 −1 81115566 81130008 ATP5S −0.234782015 0.668167795 9.47E−10 chr14 1 50779047 50792668 THEM4 −0.305755807 0.665088298 5.75E−08 chr1 −1 151846060 151882284 VANGL1 −0.35350898 0.660771307 4.81E−08 chr1 1 116184612 116236312 GSG2 −0.315820574 0.660724489 7.72E−13 chr17 1 3627197 3629993 PXMP2 −0.249805307 0.6604927 2.01E−12 chr12 1 133287436 133297414 CAMSAP1 −0.232304633 0.65983507 2.37E−09 chr9 −1 138700333 138799070 ORMDL2 −0.26193862 0.658369238 2.64E−11 chr12 1 56211806 56214959 C16orf55 −0.29431772 0.658029078 4.68E−10 chr16 1 89724152 89737675 ABHD2 −0.335157092 0.653696306 0.003173566 chr15 1 89631405 89745591 ABHD2 −0.335157092 0.653593114 3.49E−05 chr15 1 89631405 89745591 MRPS28 −0.221999518 0.653297973 1.23E−08 chr8 −1 80831098 80942506 KDM1A −0.338954726 0.652790447 4.34E−13 chr1 1 23345941 23410182 PDCD11 −0.264875391 0.651431565 2.14E−14 chr10 1 105156405 105206049 C17orf79 −0.294507305 0.648892607 2.08E−16 chr17 −1 30178883 30186256 WEE1 −0.307311914 0.64758364 4.79E−09 chr11 1 9595430 9611531 PDF −0.259372491 0.646134845 1.24E−15 chr16 −1 69360816 69373513 LRSAM1 −0.226251329 0.645026571 3.85E−09 chr9 1 130213784 130265778 TNFRSF10A −0.384420552 0.644106779 2.33E−10 chr8 −1 23048064 23082639 C16orf88 −0.272202349 0.641570896 1.77E−12 chr16 −1 19717676 19726362 PLK4 −0.310709849 0.64050983 4.03E−08 chr4 1 128802016 128820350 DPCD −0.218924523 0.640383481 3.65E−14 chr10 1 103348045 103369425 KIAA0895 −0.386314449 0.639717652 5.70E−08 chr7 −1 36363830 36429734 DDX55 −0.261862563 0.636292468 2.73E−09 chr12 1 124086672 124105480 GPHN −0.351868464 0.635572263 9.51E−09 chr14 1 66974125 67648515 WDR36 −0.308089573 0.630736331 2.57E−06 chr5 1 110427414 110469906 CKLF −0.238225994 0.628995779 6.08E−10 chr16 1 66586470 66599975 SRD5A1 −0.316238694 0.62671946 4.38E−05 chr5 1 6633456 6669675 C6orf223 −0.349827072 0.625261279 9.74E−10 chr6 1 43968337 43972877 WDHD1 −0.221635494 0.622503019 5.83E−07 chr14 −1 55405668 55493795 SRD5A1 −0.316238694 0.617079084 1.94E−06 chr5 1 6633456 6669675 −0.379767127 0.616780661 4.66E−09 chr2 1 172864490 172947158 CSNK1E −0.238834552 0.615545315 8.09E−09 chr22 −1 38686697 38714089 UCHL5 −0.229547693 0.615538747 5.89E−05 chr1 −1 192987535 193028539 HSPD1 −0.365274716 0.61459242 2.08E−16 chr2 −1 198351305 198364771 SNORD118 −0.269386914 0.614360801 1.52E−07 chr17 −1 8076296 8079714 RANGRF −0.256581556 0.613634074 4.54E−08 chr17 1 8191989 8193403 OAS3 −0.263601714 0.613097041 0.000497052 chr12 1 113376157 113411050 EEPD1 −0.381673022 0.612662004 1.49E−10 chr7 1 36192758 36341152 AARSD1 −0.280574719 0.610173181 6.33E−13 chr17 −1 41102543 41132020 PRPF19 −0.313924275 0.610127959 5.74E−10 chr11 −1 60658220 60674056 ACP1 −0.243372223 0.609269112 1.34E−13 chr2 1 264869 278283 RAB23 −0.340951531 0.607435566 0.000229489 chr6 −1 57053607 57087078 GALK2 −0.238084648 0.606353291 1.58E−09 chr15 1 49447976 49622002 BBS2 −0.340697293 0.603768681 3.23E−07 chr16 −1 56518366 56554195 SHB −0.337673042 0.603407422 1.31E−09 chr9 −1 37919131 38069208 TALDO1 −0.391999756 0.602516825 3.62E−12 chr11 1 747329 765024 SLC27A2 −0.29609587 0.600128428 4.53E−07 chr15 1 50474394 50528592 XPO5 −0.290308924 0.600041308 1.76E−15 chr6 −1 43490072 43543812 SNORD118 −0.269386914 0.598972912 1.03E−06 chr17 −1 8076296 8079714 SLC27A2 −0.29609587 0.597913672 7.12E−06 chr15 1 50474394 50528592 CENPO −0.275635182 0.596829371 6.28E−07 chr2 1 25016014 25045245 DBR1 −0.293045877 0.595369328 0.000125338 chr3 −1 137879854 137893791 TUBGCP4 −0.329918509 0.594748243 2.94E−07 chr15 1 43663293 43698238 PSMC3IP −0.218053908 0.594210465 1.78E−07 chr17 −1 40724329 40729747 GTF3C3 −0.354411257 0.594098695 4.75E−06 chr2 −1 197627756 197664425 PCBD2 −0.351750876 0.593958149 5.27E−08 chr5 1 134240596 134296967 CSNK1E −0.238834552 0.592596824 3.95E−12 chr22 −1 38694096 38713413 DAK −0.337915954 0.592201232 2.25E−11 chr11 1 61100654 61116230 SKIL −0.332370272 0.589717331 8.30E−08 chr3 1 170075514 170110536 MMACHC −0.311345645 0.589154662 8.98E−08 chr1 1 45965725 45976739 HSPE1 −0.365274716 0.589092028 7.19E−11 chr2 1 198364718 198368181 HNRNPD −0.270498972 0.588962608 2.22E−06 chr4 −1 83273651 83295109 EEPD1 −0.381673022 0.5881191 2.96E−09 chr7 1 36192758 36341152 KARS −0.361111606 0.588087532 7.38E−12 chr16 −1 75661622 75681577 NMI −0.401380326 0.587311241 1.38E−09 chr2 −1 152126979 152146571 CSTF3 −0.245463178 0.585854628 1.22E−08 chr11 −1 33106137 33183037 PLBD1 −0.318699032 0.584355958 3.96E−06 chr12 −1 14656597 14720791 TUBA4A −0.335331285 0.583464283 4.65E−08 chr2 −1 220114433 220118754 ANAPC7 −0.358004942 0.582975355 0.000285228 chr12 −1 110813276 110841535 RABEPK −0.32443941 0.580856648 1.46E−11 chr9 1 127962882 127996334 USP18 −0.352213294 0.576400343 0.000134886 chr22 1 18632666 18660164 CSTF1 −0.293961713 0.576301697 1.70E−06 chr20 1 54967450 54979518 SRPK2 −0.301338383 0.576069908 2.27E−05 chr7 −1 104756823 105029341 GPHN −0.351868464 0.575370798 3.47E−06 chr14 1 66974125 67648515 RAB15 −0.275394533 0.574973153 1.31E−06 chr14 −1 65412532 65438875 SLC48A1 −0.243259292 0.574186473 1.81E−11 chr12 1 48166991 48176536 PHB −0.271234016 0.570779776 2.66E−13 chr17 −1 47481414 47492242 GLRX3 −0.468137547 0.569271144 9.83E−14 chr10 1 131934663 131978640 THEM4 −0.305755807 0.567911313 2.03E−08 chr1 −1 151846060 151882284 PSMC2 −0.335527424 0.567378112 3.29E−13 chr7 1 102985361 103009842 RAD18 −0.294092376 0.566055082 1.34E−08 chr3 −1 8918760 9005186 ASPSCR1 −0.429796139 0.565948199 9.92E−09 chr17 1 79935426 79975280 FLVCR1 −0.328081085 0.564259882 0.000216633 chr1 1 213031597 213072705 PDCD11 −0.264875391 0.563950729 2.64E−13 chr10 1 105156405 105206049 C13orf34 −0.282975063 0.563850235 2.24E−05 chr13 1 73302064 73330318 SDCCAG3 −0.252078076 0.563677408 1.29E−10 chr9 −1 139296377 139305061 CAMSAP1 −0.232304633 0.563552316 6.26E−10 chr9 −1 138700333 138799070 HIBADH −0.435762995 0.563421604 1.48E−09 chr7 −1 27565061 27702614 SNORD118 −0.269386914 0.562529551 5.45E−05 chr17 −1 8076296 8079714 SHB −0.337673042 0.562519134 1.74E−08 chr9 −1 37919131 38069208 SPC24 −0.293998387 0.561276565 2.40E−09 chr19 −1 11256170 11266458 PSMD1 −0.289671601 0.560442291 5.62E−08 chr2 1 231921578 232037541 KIAA0319 −0.293263452 0.560086475 3.06E−07 chr6 −1 24544335 24646383 AARS −0.450373223 0.559649047 1.53E−08 chr16 −1 70286290 70323409 THEM4 −0.305755807 0.558859828 1.16E−07 chr1 −1 151846060 151882284 KIAA1324 −0.344894338 0.558749164 8.48E−05 chr1 1 109656729 109745853 PERP −0.420881809 0.557602481 5.89E−12 chr6 −1 138411923 138428648 PPP2R1B −0.269985557 0.556957945 8.20E−05 chr11 −1 111597632 111637169 SAAL1 −0.305825846 0.556790357 1.68E−08 chr11 −1 18101893 18127638 BLVRA −0.385001907 0.556720097 0.001013 chr7 1 43798279 43846938 WDR5B −0.27939038 0.556270901 5.77E−09 chr3 −1 122130715 122134882 MAP7 −0.232419099 0.556258136 1.51E−10 chr6 −1 136663875 136871646 KARS −0.361111606 0.556208481 2.59E−14 chr16 −1 75661622 75681577 G2E3 −0.281280373 0.555054321 4.91E−05 chr14 1 31028364 31089269 RAB15 −0.275394533 0.552892366 2.21E−06 chr14 −1 65412532 65438875 COPS2 −0.238084648 0.552774759 3.12E−10 chr15 −1 49417473 49447854 JHDM1D −0.36915146 0.552690772 9.23E−05 chr7 −1 139784546 139876835 TNFRSF10A −0.384420552 0.552397645 1.81E−08 chr8 −1 23048064 23082639 PERP −0.420881809 0.552162584 3.12E−07 chr6 −1 138411923 138428648 CCDC77 −0.243970997 0.551616519 3.47E−06 chr12 1 510742 551811 DAP3 −0.3152206 0.5514731 3.17E−10 chr1 1 155658849 155708801 ZNF643 −0.295962761 0.550135812 7.09E−08 chr1 1 40916716 40929390 ABHD2 −0.335157092 0.549133592 0.00095956 chr15 1 89631405 89745591 NSUN2 −0.316238694 0.547973307 1.07E−08 chr5 −1 6599352 6633404 LRRC2 −0.24589671 0.545930975 4.28E−05 chr3 −1 46556913 46608040 TARS −0.325532408 0.545403969 4.90E−11 chr5 1 33440802 33468038 HSPD1 −0.365274716 0.545028989 9.50E−09 chr2 −1 198351305 198364771 UBXN10 −0.339943828 0.545015477 0.000237589 chr1 1 20512578 20522541 KLHDC5 −0.250846871 0.54386595 5.97E−08 chr12 1 27933187 27955972 MRPL16 −0.309271189 0.542900113 4.97E−11 chr11 −1 59573612 59578345 TGEBR2 −0.323538725 0.542447072 6.66E−06 chr3 1 30647994 30735626 F3 −0.316302039 0.541670859 1.79E−05 chr1 −1 94994781 95007356 G2E3 −0.281280373 0.540537962 4.57E−05 chr14 1 31028364 31089269 G2E3 −0.281280373 0.540499443 4.34E−05 chr14 1 31028364 31089269 SLC48A1 −0.243259292 0.539334496 8.38E−13 chr12 1 48166991 48176536 BLVRA −0.385001907 0.538601989 0.000539254 chr7 1 43798279 43846938 C2orf15 −0.287652418 0.538425806 2.93E−06 chr2 1 99797542 99814089 PGM2L1 −0.340496727 0.537717149 1.93E−08 chr11 −1 74041361 74109502 MAP7 −0.232419099 0.535524202 3.31E−10 chr6 −1 136663875 136871646 WDR36 −0.308089573 0.533711417 4.59E−06 chr5 1 110427414 110469906 UBE3C −0.265141265 0.53369635 2.72E−07 chr7 1 156931607 157062066 G2E3 −0.281280373 0.533312322 0.000430128 chr14 1 31028364 31089269 POLQ −0.344922003 0.532851832 1.71E−06 chr3 −1 121150278 121264853 RIF1 −0.333349128 0.532243411 0.000275302 chr2 1 152266397 152331902 SLC2A8 −0.332165555 0.532082027 2.22E−09 chr9 1 130159421 130170177 IDE −0.323456458 0.530349431 8.90E−05 chr10 −1 94211441 94333833 IDE −0.323456458 0.527778534 8.94E−06 chr10 −1 94211441 94333833 FAM175A −0.267694635 0.527678846 8.93E−05 chr4 −1 84382092 84406334 ADRM1 −0.375468714 0.525209562 5.28E−10 chr20 1 60878061 60883918 SMPD4 −0.374036738 0.523732921 3.13E−10 chr2 −1 130908981 130939166 MSH3 −0.33197287 0.52223272 1.97E−06 chr5 1 79950467 80172279 NENF −0.26975275 0.521863544 2.26E−10 chr1 1 212606229 212619714 ESF1 −0.253283591 0.521398107 0.000347678 chr20 −1 13694969 13765532 RNMTL1 −0.390282429 0.520492511 4.85E−11 chr17 1 685513 695749 NAA16 −0.466228772 0.519873768 1.55E−06 chr13 1 41885341 41951166 TROAP −0.329360048 0.519505155 3.18E−08 chr12 1 49716971 49725514 DDX50 −0.41851803 0.518688101 1.26E−10 chr10 1 70661034 70706603 POLH −0.290308924 0.516497497 2.30E−06 chr6 1 43543887 43583397 CEP57 −0.236391887 0.515608821 2.49E−05 chr11 1 95523642 95565854 SQLE −0.412483745 0.515297147 9.81E−06 chr8 1 126010720 126034525 HNRNPA3 −0.345567093 0.514475268 2.48E−08 chr2 1 178077291 178084813 SERBP1 −0.29363511 0.513845306 9.16E−11 chr1 −1 67873493 67896098 PATL1 −0.267856683 0.513761723 1.32E−07 chr11 −1 59404194 59436511 NARF −0.327711968 0.513555641 8.18E−11 chr17 1 80416540 80446141 UTP23 −0.374374515 0.512941457 0.000967853 chr8 1 117778742 117786923 EIF2A −0.341781166 0.512176892 2.46E−13 chr3 1 150264481 150302029 DNAJC15 −0.306451735 0.512159081 5.87E−06 chr13 1 43597339 43683045 CCIAD2 −0.368241675 0.511834242 1.65E−07 chr4 −1 48887036 48908845 GLS2 −0.369251024 0.511815027 9.12E−07 chr12 −1 56864736 56882181 EXTL2 −0.246561032 0.5117553 1.09E−05 chr1 −1 101337943 101361554 NIP7 −0.259372491 0.509836595 0.000103073 chr16 1 69373343 69377014 ERGIC2 −0.316674815 0.509704344 1.46E−07 chr12 −1 29493601 29534143 GNPDA1 −0.38158971 0.509463122 1.90E−09 chr5 −1 141380234 141392596 NIP7 −0.259372491 0.509384558 1.20E−06 chr16 1 69373343 69377014 ACLY −0.31253498 0.509338512 2.67E−06 chr17 −1 40023161 40075240 C19orf20 −0.283915594 0.5082567 2.14E−06 chr19 1 507497 519423 CARS2 −0.279867021 0.507573136 4.90E−10 chr13 −1 111293787 111358485 DEAF1 −0.256741648 0.506175515 4.41E−09 chr11 −1 644225 695047 PYCRL −0.292749271 0.506005001 8.75E−09 chr8 −1 144686229 144691784 NCBP2 −0.35437085 0.505677709 1.12E−07 chr3 −1 196662278 196669468 EXOC6 −0.394254414 0.505488218 1.56E−09 chr10 1 94608277 94819247 MIOS −0.309348638 0.505485258 1.18E−07 chr7 1 7606503 7647127 PMPCA −0.252078076 0.504592963 1.43E−11 chr9 1 139305112 139318213 FAM188B −0.365084074 0.504093174 1.07E−09 chr7 1 30811033 30932002 RPL12 −0.226251329 0.504038829 2.68E−15 chr9 −1 130209953 130213684 ABHD2 −0.335157092 0.503105943 1.87E−05 chr15 1 89631405 89745591 ERCC8 −0.28157772 0.502902619 7.80E−08 chr5 −1 60169659 60240878 EIF3G −0.292801028 0.50208106 6.02E−13 chr19 −1 10225690 10230599 RPL12 −0.226251329 0.501680489 1.47E−13 chr9 −1 130209953 130213684 FUT10 −0.255860029 0.500133393 7.96E−06 chr8 −1 33228342 33330664 SARNP −0.26193862 0.49998192 2.31E−08 chr12 −1 56146247 56211540 RNF24 −0.283461559 0.498475347 3.84E−09 chr20 −1 3912068 3996036 NENF −0.26975275 0.497927553 3.13E−09 chr1 1 212606229 212619714 HSD3B7 −0.20314982 0.497791955 8.86E−09 chr16 1 30996532 31000473 FAT1 −0.290272493 0.497178271 7.11E−08 chr4 −1 187508937 187645009 PATL1 −0.267856683 0.496677553 8.77E−08 chr11 −1 59404194 59436511 PATL1 −0.267856683 0.496018831 7.54E−07 chr11 −1 59404194 59436511 MYO6 −0.43883682 0.493770242 4.95E−09 chr6 1 76458926 76626329 RNF24 −0.283461559 0.493276553 4.34E−09 chr20 −1 3912068 3996036 EBPL −0.364898082 0.491023884 1.63E−10 chr13 −1 50234862 50265611 SAR1A −0.349589716 0.488254276 3.95E−05 chr10 −1 71909960 71930279 RPL12 −0.226251329 0.488070209 8.37E−15 chr9 −1 130209953 130213684 RWDD2B −0.329455475 0.48547073 5.22E−10 chr21 −1 30376705 30391699 HMGCS1 −0.296054138 0.48520563 0.026796939 chr5 −1 43289497 43313595 DHX30 −0.356915978 0.484514643 5.69E−09 chr3 1 47844418 47891683 TGFBR2 −0.323538725 0.483851636 7.60E−09 chr3 1 30647994 30735626 PCYT2 −0.261073405 0.48298277 1.54E−10 chr17 −1 79862092 79869294 DPY19L4 −0.354808816 0.48269307 1.53E−05 chr8 1 95732103 95806076 METFL13 −0.251305655 0.482391769 1.45E−12 chr1 1 171750822 171766857 ANGEL2 −0.386058099 0.482231251 0.000348994 chr1 −1 213165524 213189168 SNRNP70 −0.352072025 0.481756432 2.30E−06 chr19 1 49588465 49611869 HNRNPU −0.307777645 0.481442138 8.09E−07 chr1 −1 245014468 245027844 MYEOV −0.477263493 0.4794864 3.63E−05 chr11 1 69061622 69064753 GLS −0.260544126 0.478984396 0.004847239 chr2 1 191745560 191800015 NUFIP1 −0.272420763 0.476234013 2.43E−05 chr13 −1 45513384 45563618 QRSL1 −0.385770406 0.47593703 7.41E−07 chr6 1 107077453 107116292 WHSC2 −0.329016517 0.474360834 3.15E−08 chr4 −1 1984441 2011837 IFT122 −0.326575154 0.472953894 1.15E−08 chr3 1 129158968 129239194 PSMC6 −0.25403134 0.472037128 8.04E−08 chr14 1 53173890 53195305 STAT1 −0.350388411 0.471996848 0.011723869 chr2 −1 191840263 191878894 PSMD1 −0.289671601 0.471330535 5.17E−11 chr2 1 231921578 232037541 SRPK2 −0.301338383 0.471067024 0.000251176 chr7 −1 104756823 105029341 PSMD4 −0.258106107 0.470437047 7.03E−10 chr1 1 151227179 151239955 FBXO45 −0.228407257 0.470374179 3.92E−07 chr3 1 196295559 196315930 ANAPC7 −0.358004942 0.466614689 3.64E−13 chr12 −1 110811283 110841535 PDXK −0.451405538 0.462928243 3.75E−11 chr21 1 45138978 45182188 TWSG1 −0.325962433 0.461428286 0.019144724 chr18 1 9334765 9402418 DHX30 −0.356915978 0.460971725 5.79E−09 chr3 1 47844418 47891683 CGREF1 −0.258522541 0.45945758 4.50E−05 chr2 −1 27323466 27341971 LRSAM1 −0.226251329 0.459400767 1.45E−08 chr9 1 130213784 130265778 VPS13C −0.315743995 0.45901679 2.17E−10 chr15 −1 62144588 62352672 RBM33 −0.265224591 0.458894378 9.05E−06 chr7 1 155437145 155493877 CEP57 −0.236391887 0.45813928 0.000680789 chr11 1 95523642 95565854 CHAC1 −0.283992403 0.457769412 5.45E−06 chr15 1 41245347 41248717 METTL13 −0.251305655 0.457647306 6.66E−08 chr1 1 171750822 171766857 C1orf56 −0.421783765 0.457335739 4.92E−07 chr1 1 151020216 151023896 FKBP3 −0.287514591 0.457295949 1.11E−08 chr14 −1 45584803 45604522 FAMI28B −0.374036738 0.456777094 2.41E−12 chr2 1 130939501 130948300 SNRNP25 −0.216414146 0.456271737 3.45E−07 chr16 1 103010 107669 PBX4 −0.31001759 0.455464005 4.84E−06 chr19 −1 19672524 19729725 PITPNB −0.261582202 0.454472217 8.06E−12 chr22 −1 28247657 28315256 DDX49 −0.343473643 0.454137569 3.16E−10 chr19 1 19030494 19039436 H2AFJ −0.277804935 0.452317978 1.43E−07 chr12 1 14927349 14927957 WDHD1 −0.221635494 0.450955613 2.73E−07 chr14 −1 55405668 55493795 BLVRA −0.385001907 0.450125531 0.001227454 chr7 1 43798279 43846938 COPS2 −0.238084648 0.449761157 5.06E−05 chr15 −1 49417473 49447854 GOPC −0.335694969 0.447666995 0.00084461 chr6 −1 117881432 117923691 CCT5 −0.247574331 0.446863757 4.61E−05 chr5 1 10250033 10266524 −0.225423721 0.445470046 1.41E−06 chr6 −1 31937587 31940069 GCFC1 −0.29229425 0.445395323 0.003627747 chr21 −1 34106210 34144169 PSMB6 −0.358538208 0.444510931 1.92E−08 chr17 1 4699439 4701798 LARP4 −0.441920352 0.442904134 0.009336652 chr12 1 50794650 50873779 RSPH1 −0.242063683 0.440651569 0.003651772 chr21 −1 43892596 43916464 GLS2 −0.369251024 0.44042743 8.53E−08 chr12 −1 56864736 56882181 NFYA −0.281763826 0.43942414 0.000194862 chr6 1 41040684 41067715 CEP57 −0.236391887 0.438163164 2.08E−05 chr11 1 95523642 95565854 SERBP1 −0.29363511 0.437109958 3.01E−13 chr1 −1 67873493 67896098 FUBP1 −0.269302108 0.43558565 2.65E−07 chr1 −1 78414090 78444770 METTL13 −0.251305655 0.434308428 1.86E−11 chr1 1 171750822 171766857 ERAL1 −0.285253889 0.433867022 9.57E−08 chr17 1 27182020 27188085 GCFC1 −0.29229425 0.433411711 0.000978954 chr21 −1 34106210 34144169 RNF24 −0.283461559 0.431234651 4.60E−09 chr20 −1 3912068 3996036 ATXN3 −0.290804143 0.431069467 0.000479918 chr14 −1 92529926 92572954 WHSC2 −0.329016517 0.430867751 1.79E−09 chr4 −1 1984441 2011837 PSMG2 −0.224568396 0.430649254 2.36E−10 chr18 1 12702425 12725739 DBR1 −0.293045877 0.430294324 0.000126091 chr3 −1 137879854 137893791 TXLNA −0.312574182 0.429015227 2.44E−06 chr1 1 32645287 32663886 RAGE −0.309361173 0.428032828 0.000150291 chr14 −1 102695179 102771531 H2AFJ −0.277804935 0.426395076 4.28E−07 chr12 1 14927349 14927957 CSNK1E −0.238834552 0.426324208 9.75E−08 chr22 −1 38686697 38714089 PSMD4 −0.258106107 0.426283039 4.96E−13 chr1 1 151227179 151239955 CCDC21 −0.299934485 0.423797272 1.75E−05 chr1 1 26560693 26605299 MAPKAPK3 −0.274974325 0.423341104 1.98E−09 chr3 1 50649339 50686720 LRFN4 −0.259494829 0.422673626 9.81E−08 chr11 1 66624589 66627946 FKTN −0.271056262 0.422275567 1.91E−06 chr9 1 108320411 108403399 SRD5A1 −0.316238694 0.421586602 3.96E−07 chr5 1 6633456 6669675 TMCO7 −0.290844829 0.419900342 4.38E−10 chr16 1 68877509 69119083 MRPL15 −0.322838359 0.417494082 1.40E−09 chr8 1 55047781 55061074 ANKRD26 −0.331205651 0.414889391 6.58E−08 chr10 −1 27293227 27389421 CENPV −0.284513729 0.114773621 8.75E−06 chr17 −1 16245848 16256813 MANIB1 −0.224377818 0.414577635 1.90E−09 chr9 1 139981400 140003635 GPR137B −0.287704623 0.41343648 0.002490864 chr1 1 236305832 236372206 TUBA1B −0.257364469 0.413380925 3.32E−11 chr12 −1 49521569 49525304 PPP2R1B −0.269985557 0.413330128 0.002196055 chr11 −1 111608605 111637169 MYO6 −0.43883682 0.413076045 2.59E−05 chr6 1 76458926 76626329 SEC23B −0.340659075 0.412925431 6.01E−07 chr20 1 18488199 18542059 MED1 −0.316078763 0.412748577 1.69E−05 chr17 −1 37560538 37607521 GCLC −0.285342884 0.412461851 1.99E−06 chr6 −1 53362139 53409927 G2E3 −0.281280373 0.412202783 8.47E−05 chr14 1 31028364 31089269 ASNA1 −0.326548953 0.411954217 2.09E−09 chr19 1 12848306 12859137 FBXO45 −0.228407257 0.411111387 0.001202472 chr3 1 196295559 196315930 AIDA −0.275078992 0.411005275 6.27E−06 chr1 −1 222841355 222885866 NUP50 −0.566797098 0.41089471 0.002087528 chr22 1 45559722 45583892 DAG1 −0.222775171 0.410793593 1.99E−08 chr3 1 49507565 49573044 WDR33 −0.366636769 0.410661679 4.42E−06 chr2 −1 128520107 128568745 ATP5S −0.234782015 0.410429584 1.63E−08 chr14 1 50779047 50792668 SERBP1 −0.29363511 0.40990949 1.06E−06 chr1 −1 67873493 67896098 LARP4 −0.441920352 0.409370756 0.00012349 chr12 1 50794650 50873779 MITD1 −0.287652418 0.409288185 0.000627109 chr2 −1 99778410 99797390 SRPK2 −0.301338383 0.40923956 5.57E−07 chr7 −1 104756823 105029341 ACP1 −0.243372223 0.407652934 4.50E−11 chr2 1 264869 278283 FAM188B −0.365084074 0.407179109 1.56E−07 chr7 1 30811033 30932002 UBXN10 −0.339943828 0.405868745 0.000361623 chr1 1 20512578 20522541 PLOD3 −0.257219677 0.405471045 6.15E−06 chr7 −1 100849258 100860954 XRCC6 −0.35122645 0.404207038 5.74E−10 chr22 1 42017123 42060043 STARD4 −0.329052253 0.403294903 0.003367646 chr5 −1 110831731 110848208 ADSS −0.367643975 0.40204654 5.57E−05 chr1 −1 244571796 244615436 NFYA −0.281763826 0.400910299 7.06E−05 chr6 1 41040684 41067715 IDE −0.323456458 0.400137839 1.26E−05 chr10 −1 94211441 94333833 MAPKAPK3 −0.274974325 0.399559751 7.30E−11 chr3 1 50649339 50686720 TUBA1B −0.257364469 0.39764006 1.17E−11 chr12 −1 49521569 49525304 RTEL1 −0.24942297 0.397172815 0.000235525 chr20 1 62289163 62328416 MIOS −0.309348638 0.395711772 1.02E−07 chr7 1 7606503 7647127 TMEM43 −0.273563381 0.395596061 1.91E−05 chr3 1 14166440 14185179 WDR59 −4.508959879 0.393873791 2.12E−10 chr16 −1 74907474 75019017 SLC1A4 −0.308988097 0.393835863 7.80E−05 chr2 1 65216535 65250999 ERO1L −0.337054537 0.393126588 1.28E−05 chr14 −1 53106634 53162423 CSTF3 −0.245463178 0.392469353 0.00612572 chr11 −1 33162978 33183037 PNN −0.269264438 0.391862884 0.000821701 chr14 1 39644425 39652422 CEP57 −0.236391887 0.391701161 2.18E−05 chr11 1 95523642 95565854 DCTN4 −0.216159533 0.391463511 0.000121824 chr5 −1 150088002 150138671 LTA4H −0.275723937 0.390887101 1.29E−07 chr12 −1 96394611 96429365 PSMD4 −0.258106107 0.390463362 3.88E−09 chr1 1 151227179 151239955 DPY19L3 −0.375796947 0.390436589 0.003708824 chr19 1 32897031 32975236 USE1 −0.315313456 0.390015387 1.74E−07 chr19 1 17326155 17330638 TFCP2 −0.281247247 0.390012591 1.28E−06 chr12 −1 51488624 51566664 ANXA2 −0.415910727 0.389991116 9.36E−08 chr15 −1 60639333 60690185 NUP50 −0.566797098 0.389803777 0.009832382 chr22 1 45559722 45583892 ICA1 −0.256836172 0.389788733 1.15E−05 chr7 −1 8152814 8301911 −0.247485563 0.389268676 6.31E−09 chr6 −1 31919864 31926887 ANXA2 −0.415910727 0.387716448 1.90E−07 chr15 −1 60639333 60690185 USE1 −0.315313456 0.387397591 5.59E−09 chr19 1 17326155 17330638 TBC1D30 −0.303436889 0.387149474 7.66E−05 chr12 1 65174589 65272083 C17orf81 −0.247903672 0.386971392 0.001650026 chr17 1 7155372 7163250 ANXA2 −0.415910727 0.385293336 1.32E−07 chr15 −1 60639333 60690185 PSMB1 −0.307799737 0.385149671 5.75E−08 chr6 −1 170844205 170862429 CAPN10 −0.215228659 0.383735779 0.031745836 chr2 1 241526189 241557122 USP45 −0.2938606 0.382977481 0.0006119 chr6 −1 99930137 99963365 TUBA1B −0.257364469 0.382884899 1.71E−11 chr12 −1 49521569 49525304 C20orf108 −0.316080368 0.382060596 2.77E−05 chr20 1 54933971 54943719 CREB3L2 −0.258978198 0.381502254 7.13E−06 chr7 −1 137559725 137686803 TMEM43 −0.273563381 0.379906406 1.61E−06 chr3 1 14166440 14185179 SETD3 −0.299635792 0.378960184 1.09E−10 chr14 −1 99864083 99947216 SLC6A6 −0.277217014 0.377888979 6.88E−05 chr3 1 14444120 14489696 DGCR14 −0.406673531 0.377148983 0.000197838 chr22 −1 19117792 19132197 SRPK2 −0.301338383 0.3769439 0.000935668 chr7 −1 104756823 105029341 PGM2L1 −0.340496727 0.37597791 1.58E−06 chr11 −1 74041361 74109502 GBAS −0.297503974 0.375723031 2.74E−06 chr7 1 56032274 56067874 CSTF1 −0.293961713 0.37560835 0.000731408 chr20 1 54967450 54979518 RDH10 −0.29931104 0.374837805 0.000556733 chr8 1 74207265 74237516 C3orf75 −0.321093023 0.374635121 5.13E−07 chr3 −1 47537130 47555251 ZNF318 −0.392401079 0.37456982 0.000716939 chr6 −1 43303808 43337181 ASPM −0.315933748 0.374561031 0.000568467 chr1 −1 197053258 197115824 RB1 −0.349624422 0.372437999 0.002659766 chr13 1 48877911 49056122 TTLL1 −0.409841903 0.372205802 1.55E−06 chr22 −1 43435650 43485434 TUBA1B −0.257364469 0.372082411 2.02E−10 chr12 −1 49521569 49525304 PARP9 −0.288010969 0.371424167 0.009993796 chr3 −1 122246806 122283424 PRPF3 −0.278351305 0.370578407 0.001660956 chr1 1 150293925 150325671 VANGL1 −0.35350898 0.369576977 9.03E−05 chr1 1 116184574 116240845 CLTA −0.315274216 0.369489121 2.53E−10 chr9 1 36190920 36212053 VGLL4 −0.338819195 0.367838887 3.24E−07 chr3 −1 11597544 11762220 TUBA1B −0.257364469 0.367796508 8.89E−11 chr12 −1 49521569 49525304 PYCR2 −0.293454524 0.366607393 7.67E−06 chr1 −1 226107578 226111959 GPX4 −0.259760253 0.36648499 3.54E−06 chr19 1 1103966 1106778 GCFC1 −0.29229425 0.365752243 0.000527093 chr21 −1 34106210 34144169 MAD1L1 −0.361371266 0.365192333 3.57E−05 chr7 −1 1855430 2272609 TCEB2 −0.246084148 0.365159265 7.01E−08 chr16 −1 2821415 2827251 CLTA −0.315274216 0.364342813 5.66E−11 chr9 1 36190920 36212053 SC4MOL −0.284951579 0.364122916 0.0058699 chr4 1 166248775 166264312 SLC19A2 −0.350423055 0.363204219 0.006681964 chr1 −1 169433147 169455241 C20orf108 −0.316080368 0.363008296 0.000505364 chr20 1 54933971 54943719 C20orf7 −0.253283591 0.36195865 5.21E−05 chr20 1 13765596 13799067 ZNF318 −0.392401079 0.361916452 3.92E−06 chr6 −1 43303808 43337181 ATXN3 −0.290804143 0.361728236 0.000977593 chr14 −1 92529926 92572954 GRINL1B −0.271186633 0.361708067 0.000890209 chr15 1 57884106 58006943 NCBP1 −0.251404024 0.360549399 0.000170074 chr9 1 100395908 100436030 FAM173B −0.247574331 0.359582157 2.06E−05 chr5 −1 10226845 10249998 GTPBP10 −0.279762111 0.359462858 1.46E−05 chr7 1 89975990 90020769 IQCK −0.272202349 0.358117308 0.000341889 chr16 1 19727778 19868907 CLTA −0.315274216 0.357928842 1.51E−09 chr9 1 36190920 36212053 ZMYND10 −0.292895152 0.357885771 4.82E−07 chr3 −1 50378541 50384283 PATL1 −0.267856683 0.3573634 3.71E−05 chr11 −1 59404194 59436511 CEP57 −0.236391887 0.35571577 0.000649532 chr11 1 95523642 95565854 ZNF200 −0.352071153 0.355081258 0.000246102 chr16 −1 3272325 3285175 ZEP1 −0.383919995 0.354620259 0.003933037 chr16 1 75182480 75206114 SLC6A20 −0.306220658 0.353102696 0.005740206 chr3 −1 45796942 45838027 MRPL14 −0.238958426 0.352692633 5.38E−07 chr6 −1 44081194 44095194 DGCR14 −0.406673531 0.352643911 3.36E−08 chr22 −1 19117792 19132197 DDB1 −0.337915954 0.351142185 9.35E−08 chr11 −1 61066920 61100666 PSMC3IP −0.218053908 0.350181162 1.99E−06 chr17 −1 40724329 40729747 MAP2K1 −0.322974834 0.349526006 9.39E−07 chr15 1 66679155 66783882 KIF20B −0.294123467 0.349467685 9.22E−06 chr10 1 91461367 91534696 FAM161A −0.256344752 0.348176582 6.15E−07 chr2 −1 62051991 62081278 OXSM −0.266638161 0.348153141 2.18E−06 chr3 1 25831571 25836025 TRMU −0.251563131 0.348031422 2.35E−06 chr22 1 46731322 46753237 ILKAP −0.290120143 0.347825991 1.66E−07 chr2 −1 239079042 239112370 LRRC27 −0.304569805 0.346768968 4.48E−05 chr10 1 134145658 134166899 C20orf7 −0.253283591 0.346589288 2.73E−05 chr20 1 13765596 13799067 RABL3 −0.291349005 0.34599985 0.011424525 chr3 −1 120405528 120461384 ACLY −0.31253498 0.345973529 6.07E−08 chr17 −1 40023161 40075240 SKA2 −0.223170945 0.345237026 8.62E−05 chr17 −1 57187308 57232800 ZBTB5 −0.378311546 0.345004195 8.04E−08 chr9 −1 37438111 37465396 ATP9B −0.272149419 0.344252258 0.010585229 chr18 1 76829397 77138278 CCDC90B −0.370153966 0.343294224 6.09E−05 chr11 −1 82972805 82997215 EHMT1 −0.241468906 0.343225546 0.000900769 chr9 1 140513454 140730576 TBC1D30 −0.303436889 0.341943875 0.009123351 chr12 1 65174589 65272083 PSMB1 −0.307799737 0.339851023 5.59E−09 chr6 −1 170844205 170862429 NICN1 −0.548623895 0.3393548 9.19E−05 chr3 −1 49460379 49466674 KLC2 −0.268390601 0.339339688 4.90E−05 chr11 1 66025190 66035300 ACLY −0.31253498 0.339231588 5.11E−05 chr17 −1 40023161 40075240 PDSS1 −0.502228537 0.339053762 0.000664451 chr10 1 26986588 27035727 −0.288397593 0.338119049 0.001128356 chr6 −1 32808494 32811824 MTCH2 −0.296519113 0.336986118 1.32E−06 chr11 −1 47638858 47664206 TMEM14B −0.315657653 0.336287771 2.21E−08 chr6 1 10747973 10757214 MKS1 −0.307616649 0.336036277 1.41E−01 chr17 −1 56282802 56296666 SPA17 −0.242556186 0.335215459 0.012571454 chr11 1 124543740 124564685 DPH3 −0.248616784 0.334674571 0.005501154 chr3 −1 16299485 16306479 HNRNPU −0.307777645 0.334566531 0.004764863 chr1 −1 245014468 245027844 MYO6 −0.43883682 0.333945893 0.001249815 chr6 1 76458926 76626329 IDE −0.323456458 0.331984317 1.05E−05 chr10 −1 94211441 94333833 −0.379767127 0.331949275 2.11E−05 chr2 1 172864490 172947158 PNN −0.269264438 0.331519226 0.014252964 chr14 1 39644425 39652422 SOCS4 −0.221635494 0.330469645 0.007892043 chr14 1 55493948 55516206 UCHL5 −0.229547693 0.330271841 0.001223918 chr1 −1 192984889 193028626 CCDC97 −0.216421102 0.330088065 2.35E−05 chr19 1 41816094 41830785 CENPB −0.317753428 0.329820214 0.000571519 chr20 −1 3764500 3767337 BRF2 −0.367090072 0.329649488 5.60E−05 chr8 −1 37701405 37707411 SNORA41 −0.240137026 0.329267135 4.95E−09 chr2 1 207024309 207027652 ESD −0.332233798 0.328445206 1.51E−07 chr13 −1 47345391 47371367 BRE −0.322999708 0.32838855 2.66E−08 chr2 1 28113596 28561768 C3orf75 −0.321093023 0.32821367 1.92E−08 chr3 −1 47537130 47555251 IWS1 −0.279959983 0.3278804 2.55E−05 chr2 −1 128238382 128284044 CHMP4A −0.25363203 0.327877116 1.43E−06 chr14 −1 24678787 24683075 DDX49 −0.343473643 0.327839782 1.25E−10 chr19 1 19030494 19039436 U2AF2 −0.208707084 0.327716523 0.000256825 chr19 1 56165416 56186081 FBXO22OS −0.249605837 0.327476528 5.52E−05 chr15 1 76196200 76223313 HNRNPA3 −0.345567093 0.327288323 3.38E−05 chr2 1 178077291 178084813 PIP5K1A −0.330751684 0.326954419 0.000959016 chr1 1 151171027 151222012 ST7OT3 −0.478497425 0.3267267 3.69E−05 chr7 1 116593381 116863961 MAN1B1 −0.224377818 0.326365456 1.10E−08 chr9 1 139981400 140003635 PHB −0.271234016 0.325967794 1.83E−07 chr17 −1 47481414 47492242 PTPDC1 −0.245287948 0.325809296 0.000578597 chr9 1 96793076 96872138 TMEM14B −0.315657653 0.325615385 4.11E−07 chr6 1 10747973 10757214 TFCP2 −0.281247247 0.32532495 0.000227055 chr12 −1 51488624 51566664 HNRNPU −0.307777645 0.325279473 1.31E−07 chr1 −1 245014468 245027844 TMEM18 −0.366817385 0.325126845 1.66E−05 chr2 −1 667335 677439 RBM33 −0.265224591 0.325019067 0.000924058 chr7 1 155437373 155574173 C20orf24 −0.278041821 0.324472858 2.72E−07 chr20 1 35234137 35240960 BRAP −0.374122321 0.323919498 0.003371223 chr12 −1 112079951 112123790 ARL5B −0.30954775 0.323049278 0.0226113 chr10 1 18948334 18970568 ANKRD26 −0.331205651 0.322554838 2.24E−05 chr10 −1 27293227 27389421 OSTC −0.25588477 0.322367509 1.79E−07 chr4 1 109571740 109588976 FLVCR1 −0.328081085 0.321104885 0.006568338 chr1 1 213031597 213072705 CHMP4A −0.25363203 0.321039276 0.000186079 chr14 −1 24678787 24683075 BRE −0.322999708 0.32064176 1.89E−08 chr2 1 28113596 28561768 C20orf24 −0.278041821 0.32062886 1.81E−07 chr20 1 35234137 35240960 NFYA −0.281763826 0.320626444 5.46E−05 chr6 1 41040684 41067715 COQ7 −0.338053935 0.319963007 0.002461308 chr16 1 19078921 19091417 ICMT −0.21685651 0.319637256 2.73E−07 chr1 −1 6281253 6296000 HTRA2 −0.308238889 0.319063639 6.91E−05 chr2 1 74756504 74760472 RDH10 −0.29931104 0.318836875 0.000625094 chr8 1 74207265 74237516 INCENP −0.296869408 0.318793464 0.000325907 chr11 1 61891445 61920635 PPME1 −0.304566241 0.318525884 2.34E−09 chr11 1 73882368 73965747 BAG4 −0.36579053 0.31781079 0.001960183 chr8 1 38034312 38070809 RTN4IP1 −0.385770406 0.31780948 0.005821078 chr6 −1 107019846 107077362 MED1 −0.316078763 0.317748819 0.002752309 chr17 −1 37562854 37607521 EIF2AK4 −0.289889834 0.31661428 0.001076009 chr15 1 40226347 40327797 LRRC61 −0.31760788 0.316051765 1.63E−05 chr7 1 150020352 150035192 ESD −0.332233798 0.316040888 3.64E−07 chr13 −1 47345391 47371367 C11orf83 −0.321989833 0.315797494 2.32E−05 chr11 1 62439126 62439848 SARNP −0.26193862 0.315488437 7.03E−06 chr12 −1 56146247 56211540 −0.225423721 0.314954787 3.35E−05 chr6 1 31939608 31949228 CENPV −0.284513729 0.313833197 0.000632947 chr17 −1 16245848 16256813 ESCO1 −0.274017091 0.313444684 8.62E−05 chr18 −1 19109264 19180845 KPNA4 −0.291750548 0.313284758 0.003588897 chr3 −1 160212783 160283376 −0.33891476 0.310807033 5.82E−05 chr2 1 173940570 174091874 ROCK2 −0.376931699 0.31046092 4.30E−05 chr2 −1 11319887 11484711 HTRA2 −0.308238889 0.310089328 4.67E−07 chr2 1 74756504 74760472 AKAP11 −0.303168028 0.30961878 7.45E−05 chr13 1 42846289 42897396 CCDC21 −0.299934485 0.309023043 0.000108549 chr1 1 26560693 26605299 −0.225423721 0.309006256 1.24E−05 chr6 −1 31937587 31940069 DHX57 −0.284647233 0.308522622 2.11E−05 chr2 −1 39024871 39103049 DNTTIP1 −0.303772028 0.307559527 0.003022301 chr20 1 44420576 44440066 ETAA1 −0.328099626 0.307153729 0.00069992 chr2 1 67624451 67637677 CNIH4 −0.286188384 0.306598143 0.00423316 chr1 1 224544552 224567154 PRPSAP1 −0.254262624 0.306011283 1.17E−07 chr17 −1 74307014 74350230 HEXA −0.324343034 0.305820942 0.000102138 chr15 −1 72635775 72668817 PDSS2 −0.245888559 0.305143305 0.004311838 chr6 −1 107585390 107780768 GPR19 −0.328224193 0.304496347 3.32E−05 chr12 −1 12813995 12849121 C3orf67 −0.324588491 0.304257849 1.46E−06 chr3 −1 58727733 59035810 BRE −0.322999708 0.304018373 3.68E−08 chr2 1 28113596 28561768 ASXL2 −0.463695644 0.303172395 0.001675772 chr2 −1 25960557 26101385 NHLRC2 −0.273346942 0.302062874 0.002122423 chr10 1 115614420 115676953 POLD3 −0.426504699 0.30196859 0.001454831 chr11 1 74303629 74353765 TRAPPC6A −0.339851214 0.301253824 2.17E−05 chr19 −1 45666187 45681485 C1orf56 −0.421783765 0.300324813 0.034014371 chr1 1 151020216 151023896 RPIA −0.309904287 0.300228981 0.00040091 chr2 1 88991162 89050427 PPP2R1B −0.269985557 0.300119404 0.000686702 chr11 −1 111608605 111637169 GPHN −0.351868464 0.300088303 0.000580681 chr14 1 66974125 67648515 PTPDC1 −0.245287948 0.29966189 0.00020657 chr9 1 96793076 96872138 MRPL49 −0.406804065 0.299548507 3.78E−07 chr11 1 64889728 64894841 MKKS −0.249140135 0.299381998 2.97E−05 chr20 −1 10385832 10414870 XYLB −0.325646114 0.298456177 0.000370036 chr3 1 38388270 38456467 MSRB2 −0.408148607 0.298049078 8.88E−06 chr10 1 23384435 23410942 PNN −0.269264438 0.297937794 0.005612002 chr14 1 39644425 39652422 CTSB −0.309186459 0.297799527 0.000725681 chr8 −1 11700033 11725738 CD81 −0.274970263 0.296499219 0.00019669 chr11 1 2398520 2418627 SEL1L3 −0.279664792 0.296454426 2.04E−06 chr4 −1 25749055 25865217 KPNA4 −0.291750548 0.295531594 8.14E−06 chr3 −1 160212783 160283376 SLC1A4 −0.308988097 0.295132955 0.00017921 chr2 1 65216535 65250999 RASL11A −0.237118658 0.295132892 0.001944027 chr13 1 27844464 27847827 ROPN1L −0.320073344 0.294441374 0.001973813 chr5 1 10441636 10465136 PYCR2 −0.293454524 0.293532102 2.40E−05 chr1 −1 226107578 226111959 SMAD2 −0.355652369 0.293105469 0.009713946 chr18 −1 45357922 45456930 HNRNPD −0.270498972 0.292946285 0.000267841 chr4 −1 83273651 83295109 GCC1 −0.281291202 0.292606877 1.24E−07 chr7 −1 127220672 127225661 SERBP1 −0.29363511 0.29218459 0.002589163 chr1 −1 67873493 67896098 ENSA −0.251337512 0.291670526 0.001771143 chr1 −1 150593727 150602072 UTP23 −0.374374515 0.291620044 0.001465454 chr8 1 117778742 117786923 ORC4L −0.238091428 0.291286758 0.010195528 chr2 −1 148691981 148778292 WDR59 −0.508959879 0.290785158 7.06E−06 chr16 −1 74907474 75019017 C20or124 −0.278041821 0.290700552 7.95E−07 chr20 1 35234137 35240960 ATP6V1H −0.354448605 0.290649641 0.000252654 chr8 −1 54628116 54755547 STK38 −0.265962322 0.290560158 0.000340764 chr6 −1 36461669 36515247 SEC23B −0.340659075 0.290445553 0.008117135 chr20 1 18488199 18542059 SOD1 −0.301587643 0.290408479 1.34E−05 chr21 1 33031935 33041244 TWSG1 −0.325962433 0.289821866 0.011350703 chr18 1 9334765 9402418 SDHC −0.268373166 0.289741367 0.000174639 chr1 1 161284047 161332984 C19orf55 −0.265538386 0.288967257 0.00432928 chr19 1 36249044 36260077 PTOV1 −0.390769905 0.288238005 0.001740157 chr19 1 50354138 50363990 NAA16 −0.466228772 0.28723025 0.02734293 chr13 1 41885341 41951166 C5orf22 −0.323327912 0.287133007 0.046141333 chr5 1 31532373 31555165 FAM76A −0.336636978 0.286145642 0.000106186 chr1 1 28052490 28089633 ZXDC −0.388243791 0.285635909 0.001098803 chr3 −1 126179926 126194708 SLC1A4 −0.308988097 0.28563389 0.003322963 chr2 1 65216535 65250999 LUC7L −0.322125243 0.2854486 0.037389133 chr16 −1 238968 279462 NCBP2 −0.35437085 0.284960143 0.000256337 chr3 −1 196662278 196669468 TNFAIP8 −0.23871888 0.284650699 0.028805426 chr5 1 118690009 118730293 TMEM216 −0.237893736 0.284623004 3.69E−06 chr11 1 61159865 61166323 PPP5C −0.301902566 0.28441208 8.58E−05 chr19 1 46850294 46894109 LARP4 −0.441920352 0.284398319 0.001096515 chr12 1 50794650 50873779 HNRNPD −0.270498972 0.28430902 0.017009884 chr4 −1 83273651 83295109 FDXACB1 −0.321542807 0.284275784 0.018503415 chr11 −1 111652919 111742004 C1orf9 −0.27026984 0.283762125 0.000215883 chr1 1 172501489 172580971 PPME1 −0.304566241 0.283613761 2.75E−08 chr11 1 73882368 73965747 RSF1 −0.244529243 0.283236748 0.013331292 chr11 −1 77371041 77531880 RFESD −0.334412968 0.281765902 3.54E−05 chr5 1 94982458 94991894 ERP29 −0.300938141 0.28169008 2.99E−05 chr12 1 112451152 112461024 L2HGDH −0.234782015 0.281457486 3.40E−06 chr14 −1 50712120 50778947 MED20 −0.306448506 0.281320908 1.23E−06 chr6 −1 41873092 41888837 SRPK2 −0.301338383 0.281293084 0.000134988 chr7 −1 104756823 105029341 COMMD5 −0.441770249 0.280633576 1.03E−05 chr8 −1 146075552 146078932 MKS1 −0.307616649 0.280311679 2.81E−05 chr17 −1 56282803 56296666 NFX1 −0.284450733 0.280039705 0.010754654 chr9 1 33290509 33371155 C2orf60 −0.324785351 0.279217588 4.81E−06 chr2 −1 200794698 200820459 MAP7 −0.232419099 0.278644953 0.000157567 chr6 −1 136663875 136871646 CMC1 −0.284020829 0.278289086 0.001866284 chr3 1 28283086 28366633 FAM24B −0.318682025 0.276598614 0.000532451 chr10 −1 124608594 124639114 IFT88 −0.265596692 0.27589642 0.000476071 chr13 1 21141208 21265501 CREB3L4 −0.210442017 0.275616911 0.004132305 chr1 1 153940379 153946839 HMGN4 −0.207414827 0.27558188 3.59E−06 chr6 1 26538639 26546482 KIAA1279 −0.257616414 0.274798022 0.000804998 chr10 1 70748487 70776738 ANAPC2 −0.294481831 0.274772021 0.002846399 chr9 −1 140069236 140082989 UTP23 −0.374374515 0.274727629 0.017033035 chr8 1 117778742 117786923 PIGB −0.44469494 0.274696365 0.000992609 chr15 1 55611133 55647845 COQ7 −0.338053935 0.272966046 0.002075319 chr16 1 19078921 19091417 PHAX −0.313178185 0.272698658 0.000989986 chr5 1 125935960 125962944 SLC31A1 −0.234494526 0.27247291 0.012793448 chr9 1 115983842 116026772 MORN2 −0.284647233 0.272345217 0.01474394 chr2 1 39103103 39109850 ISOC2 −0.343599679 0.271799885 0.003251463 chr19 −1 55964345 55973049 PIGB −0.44469494 0.271571495 0.004821511 chr15 1 55611133 55647845 TIGD1 −0.369573272 0.270320642 0.012986093 chr2 −1 233412779 233415226 ZBED3 −0.240099625 0.270062413 0.007176586 chr5 −1 76367897 76383148 FBXO45 −0.228407257 0.269760372 0.001837268 chr3 1 196295559 196315930 KIAA1704 −0.272420763 0.269304031 0.019292559 chr13 1 45563755 45607742 DLST −0.263197371 0.268984711 0.006138887 chr14 1 75348619 75370443 HMOX2 −0.261263874 0.268156798 6.75E−05 chr16 1 4526380 4560348 ENSA −0.251337512 0.268093768 0.004668268 chr1 −1 150596096 150602053 IQCE −0.339575937 0.267671879 0.006479191 chr7 1 2598632 2654368 NFX1 −0.284450733 0.267474977 0.006666736 chr9 1 33290509 33371155 PHF5A −0.322027613 0.267451505 0.007672976 chr22 −1 41855721 41864729 NDUFA7 −0.252441473 0.266811861 5.24E−06 chr19 −1 8376234 8386280 PPIL4 −0.401690896 0.266681526 0.028739864 chr6 −1 149825869 149867174 C2orf60 −0.324785351 0.266144313 0.000639377 chr2 −1 200794698 200820459 STK38 −0.265962322 0.265843616 0.001730184 chr6 −1 36461669 36515247 ASPM −0.315933748 0.265101026 0.000444641 chr1 −1 197053258 197115824 DUSP6 −0.421794981 0.263858008 0.018789761 chr12 −1 89741839 89746296 HEBP2 −0.294543757 0.262839637 1.50E−06 chr6 1 138725356 138734310 HBXIP −0.22650417 0.262706119 8.29E−06 chr1 −1 110943871 110950560 GOPC −0.335694969 0.262611678 0.015028112 chr6 −1 117881432 117923691 SMAD2 −0.355652369 0.262541292 0.000729011 chr18 −1 45357922 45456930 DCTN4 −0.216159533 0.262405287 4.65E−06 chr5 −1 150088002 150138671 GOPC −0.335694969 0.262083104 0.000305851 chr6 −1 117881432 117923691 HEBP1 −0.268525561 0.260875236 0.038292344 chr12 −1 13127803 13153221 PSMC2 −0.335527424 0.26064094 0.045816386 chr7 1 102985361 103009842 TEX264 −0.282459047 0.260376359 7.72E−06 chr3 1 51705248 51738339 NEK3 −0.308457391 0.259810753 0.02572221 chr13 −1 52706783 52733724 JOSD2 −0.29879725 0.259261204 0.0032112 chr19 −1 51009259 51014477 PTGES2 −0.27452633 0.258797215 1.42E−05 chr9 −1 130882972 130890741 EPT1 −0.286072226 0.258783558 0.001441785 chr2 1 26568982 26618759 GCLC −0.285342884 0.258395056 0.000665358 chr6 −1 53362139 53409927 COG5 −0.239778252 0.258363981 0.016099573 chr7 −1 106842189 107204485 PHAX −0.313178185 0.258144523 0.044160417 chr5 1 125935960 125962944 RPL17 −0.270500948 0.257962512 0.028497526 chr18 −1 47015796 47017814 RDH10 −0.29931104 0.257485677 0.002367952 chr8 1 74207265 74237516 C20orf108 −0.316080368 0.256922933 0.0002806 chr20 1 54933971 54943719 RPL36AL −0.310966562 0.256748947 4.44E−06 chr14 −1 50085407 50087361 WDR53 −0.228407257 0.256102911 0.001020651 chr3 −1 196281056 196295510 HNRNPD −0.270498972 0.255818394 0.001910296 chr4 −1 83273651 83295109 ZKSCAN1 −0.295926961 0.255679743 0.019872896 chr7 1 99613204 99636631 MDN1 −0.323383819 0.255635275 0.010116651 chr6 −1 90352218 90529442 COMMD5 −0.441770249 0.25550232 0.000106261 chr8 −1 146075552 146078932 IQCH −0.291086472 0.255491036 4.88E−05 chr15 1 67547169 67794142 KIAA1704 −0.272420763 0.255239159 0.048538694 chr13 1 45563755 45607742 RPS6KL1 −0.259682274 0.254390248 0.000688209 chr14 −1 75372347 75389145 ELL2 −0.363180893 0.253430294 0.022297225 chr5 −1 95220802 95297775 C4orf23 −0.315455915 0.253413485 1.93E−05 chr4 1 8442532 8478253 DAG1 −0.222775171 0.253408278 0.000211878 chr3 1 49507565 49573044 DUSP6 −0.421794981 0.253379004 0.018685938 chr12 −1 89741839 89746296 VGLL4 −0.338819195 0.25277911 0.006514183 chr3 −1 11597544 11762220 TNFAIP8 −0.23871888 0.252662179 0.022627018 chr5 1 118690009 118730293 BAG4 −0.36579053 0.251969411 0.001961102 chr8 1 38034312 38070809 EIF4E2 −0.369573272 0.251616958 6.19E−05 chr2 1 233414762 233433920 NACAP1 −0.342446473 0.251485765 1.36E−09 chr12 −1 57094565 57119083 SERBP1 −0.29363511 0.25141299 1.35E−06 chr1 −1 67873493 67896098 HMGN4 −0.207414827 0.25121774 6.81E−05 chr6 1 26538639 26546482 LAP3 −0.333762016 0.251215537 0.005772231 chr4 1 17578815 17609591 ESF1 −0.253283591 0.250955687 0.008353744 chr20 −1 13694969 13765532 TM7SF3 −0.281259298 0.249855668 0.002154465 chr12 −1 27124519 27167339 PHAX −0.313178185 0.24773213 0.046681146 chr5 1 125935960 125962944 AASDH −0.24460245 0.245784979 0.007349758 chr4 −1 57204456 57253666 HNRNPH3 −0.364665187 0.245711493 0.006079061 chr10 1 70091832 70102944 C17orf81 −0.247903672 0.245481137 0.001667237 chr17 1 7155372 7163250 COMMD5 −0.441770249 0.24460423 0.002447571 chr8 −1 146075552 146078932 IQCH −0.291086472 0.244452903 1.05E−05 chr15 1 67547169 67794142 HN1 −0.352915116 0.243996671 0.000979556 chr17 −1 73131343 73150778 MED1 −0.316078763 0.243837247 0.008788836 chr17 −1 37562854 37607521 WDR60 −0.389032296 0.243712351 0.000300271 chr7 1 158649269 158738880 DCP1A −0.37393939 0.243107657 0.015402264 chr3 −1 53317448 53381637 QRSL1 −0.385770406 0.242655501 0.033329157 chr6 1 107077453 107116292 ERCC3 −0.392019389 0.242649264 0.004948282 chr2 −1 128014866 128051752 CREB1 −0.442958754 0.242362293 0.026815326 chr2 1 208394616 208468155 IWS1 −0.279959983 0.242288644 0.000355171 chr2 −1 128238382 128284044 STX10 −0.24548072 0.242138115 6.00E−07 chr19 −1 13254903 13261052 KPNA4 −0.291750548 0.241978566 0.000978887 chr3 −1 160212783 160283376 HBXIP −0.22650417 0.241859734 0.0001587 chr1 −1 110943871 110950560 UNC93B1 −0.262448866 0.241830815 0.004974303 chr11 −1 67758575 67771593 SIK2 −0.255639754 0.241680119 0.001022483 chr11 1 111473192 111601577 IQCH −0.291086472 0.240445624 4.87E−05 chr15 1 67547169 67794142 POLL −0.218924523 0.240262076 0.00067314 chr10 −1 103338639 103347966 SPATA13 −0.406111741 0.23969374 0.012176701 chr13 1 24734887 24881210 PSMD12 −0.248429065 0.239365644 0.002533351 chr17 −1 65334032 65362743 TMEM18 −0.366817385 0.238269476 0.010915957 chr2 −1 667335 677439 FAM76B −0.236391887 0.238245555 0.022350557 chr11 −1 95502106 95522954 HNRNPA3 −0.345567093 0.237898969 0.004638488 chr2 1 178077477 178086111 NDUFS8 −0.248581907 0.237816023 0.008569348 chr11 1 67798094 67804114 UBA52 −0.303994501 0.237743741 2.01E−08 chr19 1 18682614 18688269 TM7SF3 −0.281259298 0.237387852 0.004970843 chr12 −1 27124519 27167339 RTN4IP1 −0.385770406 0.236305218 0.028704102 chr6 −1 107019846 107077362 SPATA13 −0.406111741 0.235469392 0.002410546 chr13 1 24734861 24798936 RIF1 −0.333349128 0.235074379 0.02790839 chr2 1 152266455 152333863 ZNF428 −0.270702519 0.233993112 0.000942811 chr19 −1 44111377 44124006 EIF4E2 −0.369573272 0.233736252 0.000298064 chr2 1 233414762 233433920 SEL1L3 −0.279664792 0.23345406 0.000110772 chr4 −1 25749055 25865217 MIB2 −0.251711462 0.233070065 0.014264956 chr1 1 1550884 1565985 PDXK −0.451405538 0.232657066 8.42E−05 chr21 1 45138978 45182188 NACAP1 −0.342446473 0.231993323 4.49E−09 chr12 −1 57094565 57119083 NDUFS8 −0.248581907 0.231799343 0.000342283 chr11 1 67798094 67804114 CBLL1 −0.319197999 0.230551304 0.031055773 chr7 1 107384142 107400029 LRRC2 −0.24589671 0.229714562 0.00157909 chr3 −1 46556913 46608040 IQCE −0.339575937 0.229341828 0.018805575 chr7 1 2598632 2654368 MOCOS −0.26317804 0.229136307 0.00167835 chr18 1 33767482 33852120 RTEL1 −0.24942297 0.228977279 0.000153908 chr20 1 62289163 62327606 −0.247485563 0.228857324 4.31E−06 chr6 1 31926857 31937532 POLR2L −0.32790758 0.228740978 0.00633064 chr11 −1 839721 842545 SDHC −0.268373166 0.228249718 0.001145497 chr1 1 161284047 161332984 TEX264 −0.282459047 0.227925078 6.47E−05 chr3 1 51705248 51738339 ENO3 −0.239178 0.22767744 0.001851468 chr17 1 4854390 4860426 SETD3 −0.299635792 0.227594182 0.000663135 chr14 −1 99876141 99947125 TEX264 −0.282459047 0.227145496 9.38E−05 chr3 1 51705248 51738339 ATP5S −0.234782015 0.226774004 0.014577283 chr14 1 50779047 50789743 ROCK2 −0.376931699 0.225720089 0.002372911 chr2 −1 11319887 11484711 FOXN2 −0.296549353 0.225405722 0.004958872 chr2 1 48541849 48606433 WDR59 −0.508959879 0.225202159 0.001611494 chr16 −1 74907474 75019017 FAM161A −0.256344752 0.225159978 0.000203183 chr2 −1 62051991 62081278 −0.286391544 0.224339418 0.022441647 chr1 1 233463514 233520894 ZNF589 −0.308092571 0.224088382 0.01320704 chr3 1 48282590 48312477 CAPN10 −0.215228659 0.223593268 0.00293259 chr2 1 241526133 241538526 CTSB −0.309186459 0.223326074 0.001251129 chr8 −1 11700033 11725738 DNTTIP1 −0.303772028 0.223253012 0.005562276 chr20 1 44420576 44440066 RWDD4A −0.367487665 0.221987754 0.000431143 chr4 −1 184560788 184580378 ENSA −0.251337512 0.220849497 0.017954766 chr1 −1 150599530 150602053 ADK −0.241940696 0.220179424 0.011099027 chr10 1 75936444 76469061 SLC1A4 −0.308988097 0.21984612 0.003014375 chr2 1 65216535 65250999 CD2BP2 −0.246901578 0.218720419 8.93E−06 chr16 −1 30362087 30366682 CNIH4 −0.286188384 0.218572814 0.007465584 chr1 1 224544552 224567154 RTEL1 −0.24942297 0.218236696 0.012312633 chr20 1 62289163 62327606 −0.330163571 0.217938644 3.80E−06 chr6 −1 31694815 31698394 ZNF697 −0.285615275 0.217890916 0.026932223 chr1 −1 120162000 120190390 MBD4 −0.326575154 0.217830565 0.040163792 chr3 −1 129149787 129158872 C1orf58 −0.275078992 0.217719245 0.028287267 chr1 1 222885895 222908538 MOSPD3 −0.301219721 0.216523212 0.000442534 chr7 1 100209725 100212949 AASDH −0.24460245 0.21611587 0.021452164 chr4 −1 57204456 57253666 C2orf47 −0.324785351 0.21589926 0.000312216 chr2 1 200820326 200828848 MMADHC −0.265383202 0.215158501 3.39E−07 chr2 −1 150426148 150444330 WDR33 −0.366636769 0.214378714 0.001006555 chr2 −1 128458596 128568721 LSM11 −0.239070625 0.213103159 0.015851834 chr5 1 157170755 157187717 FN3KRP −0.258605213 0.213007101 0.034290656 chr17 1 80674582 80685892 NCBP1 −0.251404024 0.21266354 0.011140508 chr9 1 100395908 100436030 UQCC −0.318513573 0.212363978 0.003763106 chr20 −1 33890369 33999944 RBM33 −0.265224591 0.212273402 0.003736565 chr7 1 155437373 155574173 C16orf88 −0.272202349 0.211548111 4.71E−05 chr16 −1 19717676 19726362 SERBP1 −0.29363511 0.211459771 0.017562036 chr1 −1 67873493 67896098 HIST1H3I −0.253736937 0.211366113 0.0039775 chr6 −1 27839683 27840093 NAGLU −0.361867945 0.210599622 0.004873705 chr17 1 40687951 40696464 ZNF668 −0.282985758 0.210132911 0.00037216 chr16 −1 31072171 31085577 BAG4 −0.36579053 0.20886034 0.010375397 chr8 1 38034312 38070809 C2orf79 −0.275635182 0.208635961 0.000349842 chr2 −1 25012855 25016251 ARL5B −0.30954775 0.208538989 0.008971183 chr10 1 18948334 18970568 ARG2 −0.353923274 0.208130192 0.009724127 chr14 1 68086579 68118437 BRD9 −0.391690922 0.207933989 2.05E−06 chr5 −1 864238 892661 PRPF4B −0.258675393 0.207736724 0.048433746 chr6 1 4021560 4062141 TMEM79 −0.28814387 0.207702924 0.000589245 chr1 1 156252739 156262234 ZBED3 −0.240099625 0.207588603 0.002109014 chr5 −1 76367897 76383148 MTIF3 −0.308984575 0.207096259 0.000235207 chr13 −1 28009780 28024701 HNRNPA3 −0.345567093 0.207065767 0.035969594 chr2 1 178077477 178086111 PRPF4B −0.258675393 0.206775918 0.0007869 chr6 1 4021560 4062141 RBM33 −0.265224591 0.206292959 0.004885864 chr7 1 155437145 155493877 BEAR −0.345325231 0.205916784 0.005229164 chr16 1 14726672 14763093 RPS15 −0.366521564 0.204812055 7.34E−08 chr19 1 1438363 1440492 RNASEN −0.323327912 0.204735252 0.001757762 chr5 −1 31401169 31532168 TMED9 −0.362181166 0.204379838 0.002121877 chr5 1 177019159 177023125 DRAP1 −0.304144949 0.203963513 0.007475415 chr11 1 65686728 65689031 HMGN4 −0.207414827 0.203301495 0.000785941 chr6 1 26538639 26546482 SDHC −0.268373166 0.20271015 7.45E−05 chr1 1 161284047 161332984 MED20 −0.306448506 0.201491874 0.003856186 chr6 −1 41873092 41888837 ARL6IP1 −0.255299482 0.201133664 0.005341398 chr16 −1 18802991 18812917 FXC1 −0.400110753 0.200816677 0.040990593 chr11 1 6502690 6505909 ENSA −0.251337512 0.200682675 0.00273695 chr1 −1 150596096 150602053 ASF1A −0.293415186 0.200449032 0.024567634 chr6 1 119215384 119230332 TSSC4 −0.25495048 0.198841744 0.000696997 chr11 1 2421718 2425106 CISH −0.274974325 0.198661891 0.000494064 chr3 −1 50643927 50649203 C6orf130 −0.281763826 0.198582257 0.002808047 chr6 −1 41032517 41040330 ENAH −0.297371742 0.198191826 0.00638419 chr1 −1 225680538 225840844 COG5 −0.239778252 0.196879153 0.026218096 chr7 −1 106842189 107204485 CISH −0.274974325 0.195952875 0.000347984 chr3 −1 50643927 50649203 SFT2D3 −0.331824877 0.1956986 0.001228807 chr2 1 128458597 128461385 DEPDC6 −0.319715962 0.195268925 0.045207173 chr8 1 120885900 121063157 CDC20B −0.383282634 0.193396674 0.001607889 chr5 −1 54408823 54469003 LUC7L −0.322125243 0.193382226 0.008404655 chr16 −1 238968 279462 ECHDC1 −0.355326207 0.193281817 0.035310513 chr6 −1 127609857 127664745 LARP4 −0.441920352 0.192714139 0.009855961 chr12 1 50794650 50873779 SLC38A7 −0.287708322 0.192191172 0.016466806 chr16 −1 58699013 58718674 ZNF709 −0.333291789 0.192095306 0.047148109 chr19 −1 12571998 12595643 EHMT1 −0.241468906 0.191928566 0.006694348 chr9 1 140513454 140730576 C3orf19 −0.365475119 0.191633864 0.037208297 chr3 1 14693271 14714166 FBXO34 −0.310537562 0.190408434 0.004968945 chr14 1 55738021 55820329 SOCS4 −0.221635494 0.190363551 0.030552367 chr14 1 55493948 55516206 MBD4 −0.326575154 0.190101405 0.030399016 chr3 −1 129149787 129158872 ZNF828 −0.247162136 0.189606014 0.004731333 chr13 1 115079988 115092796 FAM76B −0.236391887 0.188895264 0.031508416 chr11 −1 95502106 95522954 TMED2 −0.238864154 0.188736288 0.031601869 chr12 1 124069076 124082681 RAB11FIP5 −0.23740607 0.188692829 0.002314502 chr2 −1 73300510 73340146 RTN3 −0.273559188 0.187729043 0.000640369 chr11 1 63448922 63527337 RAB22A −0.257197954 0.187606344 0.009278068 chr20 1 56884752 56942563 RPL17 −0.270500948 0.187496627 0.000316926 chr18 −1 47014858 47018906 LUC7L −0.322125243 0.187482062 0.008875607 chr16 −1 238968 279462 E4F1 −0.314780615 0.187463536 0.007604251 chr16 1 2273567 2285743 NFYA −0.281763826 0.187323516 0.006454767 chr6 1 41040684 41067715 RPL27 −0.290548908 0.18694156 6.81E−06 chr17 1 41150446 41154956 ECHDC1 −0.355326207 0.185879935 0.023581092 chr6 −1 127609857 127664745 POLR2H −0.289927146 0.184724665 0.002708717 chr3 1 184079506 184086382 DTX3L −0.312452653 0.184492192 0.026590419 chr3 1 122283085 122294050 ZNF839 −0.338895641 0.184191726 0.002762849 chr14 1 102786096 102809044 RAD18 −0.294092376 0.183299766 0.001102363 chr3 −1 8918760 9005186 ZNF251 −0.340718978 0.183016527 0.009696152 chr8 −1 145946295 145980970 MKLN1 −0.285004864 0.182861126 0.027872814 chr7 1 131012619 131181395 NEK3 −0.308457391 0.182527193 0.029590799 chr13 −1 52706783 52733724 ECHDC1 −0.355326207 0.182233872 0.030122483 chr6 −1 127609857 127664745 RTEL1 −0.24942297 0.18181089 0.009750693 chr20 1 62289163 62327606 GOPC −0.335694969 0.18135179 0.008913284 chr6 1 117881432 117923691 SNX25 −0.230619058 0.181321736 0.00508148 chr4 1 186125391 186285125 RPL17 −0.270500948 0.181205032 0.000336704 chr18 −1 47014858 47018906 ACOT13 −0.354368463 0.18057648 0.023336259 chr6 1 24667299 24701942 NFX1 −0.284450733 0.180005388 0.005070766 chr9 1 33290510 33365271 UBXN10 −0.339943828 0.178892308 0.016472937 chr1 1 20512578 20522541 TMED2 −0.238864154 0.178614843 0.045271549 chr12 1 124069076 124082681 PELI1 −0.263776086 0.17833332 0.004144771 chr2 −1 64319786 64371588 TMED9 −0.362181166 0.178197266 0.016340136 chr5 1 177019159 177023125 AARSD1 −0.280574719 0.177812046 0.000880047 chr17 −1 41120107 41132545 SNTB2 −0.300511266 0.177235272 0.018065978 chr16 1 69221032 69342955 TIRAP −0.323262221 0.176640436 0.002976945 chr11 1 126152982 126164828 AAGAB −0.291086472 0.175898347 0.049778227 chr15 −1 67493371 67547074 ZNHIT1 −0.257219677 0.175337489 0.008461241 chr7 1 100860949 100867471 RPL17 −0.270500948 0.175220399 0.000132726 chr18 −1 47014858 47018906 C2CD3 −0.304566241 0.174564094 0.004587842 chr11 −1 73724430 73882064 DCP1A −0.37393939 0.174172186 0.008924473 chr3 −1 53317448 53381637 SLC35F5 −0.242253514 0.172677635 0.008053508 chr2 −1 114470369 114514400 ZNF589 −0.308092571 0.17235098 0.008160301 chr3 1 48282590 48312477 C4orf41 −0.367487665 0.172272241 0.046163245 chr4 1 184580420 184634745 DUS4L −0.239778252 0.171733422 0.015329732 chr7 1 107204403 107218906 ATP9B −0.272149419 0.171598972 0.007401813 chr18 1 76829397 77138278 KLHDC10 −0.422630708 0.171455233 0.025949102 chr7 1 129710350 129773596 SDHC −0.268373166 0.170267544 0.029404858 chr1 1 161284047 161332984 DNAJC9 −0.362712454 0.169673626 0.03135362 chr10 −1 75002582 75008620 WFDC3 −0.303772028 0.169358703 0.034842302 chr20 −1 44402847 44420547 TUBG2 −0.331145925 0.168978567 0.007156872 chr17 1 40811266 40819021 HNRNPH3 −0.364665187 0.168636613 0.019803317 chr10 1 70091832 70102944 NEU3 −0.238234754 0.168607098 0.00769773 chr11 1 74699179 74718741 NDUFB2 −0.284421962 0.168594199 0.006711868 chr7 1 140396471 140422590 SUB1 −0.360871485 0.167909752 0.012598882 chr5 1 32585605 32604185 ORC4L −0.238091428 0.167153184 0.007382173 chr2 −1 148691981 148778292 CTTN −0.306355934 0.167097047 0.016552457 chr11 1 70244650 70282681 GTF2E1 −0.291349005 0.166147044 0.007656982 chr3 1 120461579 120501916 RANBP10 −0.315427602 0.165856155 0.009310847 chr16 −1 67757005 67840555 NDUFB6 −0.269773941 0.165153749 8.48E−05 chr9 −1 32552997 32573160 U2AF2 −0.208707084 0.164821088 0.005026224 chr19 1 56165416 56186081 PITPNA −0.317543209 0.164787865 0.024251008 chr17 −1 1421287 1466110 GLE1 −0.21471907 0.164688923 0.005880602 chr9 1 131267010 131302156 HOOK2 −0.247534635 0.164562585 0.012002635 chr19 −1 12873817 12886434 PDS5B −0.323312404 0.163100947 0.046015774 chr13 1 33160564 33352157 HIST1H3F −0.327602788 0.163048806 0.006703769 chr6 −1 26250423 26250833 MFAP1 −0.224961111 0.16272895 0.013987432 chr15 −1 44096690 44117000 FBXL18 −0.279247645 0.162168754 0.00104894 chr7 −1 5528880 5553382 FAU −0.406804065 0.161929641 0.000297229 chr11 −1 64888103 64889660 CDC20B −0.383282634 0.161646367 0.004442713 chr5 −1 54408823 54469003 ANAPC16 −0.236656505 0.161380554 0.001393966 chr10 1 73975806 73993587 TRAF2 −0.390824094 0.160954856 0.004567106 chr9 1 139780970 139821059 MDN1 −0.323383819 0.160289758 0.010822148 chr6 −1 90353231 90529442 MDN1 −0.323383819 0.159439627 0.025894028 chr6 −1 90353231 90529442 KLHL36 −0.287914731 0.158563684 0.017189251 chr16 1 84682107 84701292 EEPD1 −0.381673022 0.158255959 0.00114505 chr7 1 36192758 36341152 RANBP10 −0.315427602 0.158083428 0.00357063 chr16 −1 67757005 67840555 STUB1 −0.207566771 0.15766592 0.00420275 chr16 1 730276 732753 SGTA −0.377305347 0.156641041 0.000905684 chr19 −1 2755395 2783315 PARN −0.288966717 0.156584121 0.012747738 chr16 −1 14529559 14724124 AIDA −0.275078992 0.156446601 0.003998314 chr1 −1 222841355 222885866 C1orf151 −0.295885095 0.156140688 3.48E−05 chr1 1 19923484 19956314 CAMSAP1 −0.232304633 0.154584448 0.003500052 chr9 −1 138700333 138799070 GLE1 −0.21471907 0.154575495 0.048115631 chr9 1 131266979 131304567 FUBP1 −0.269302108 0.154423734 0.015358702 chr1 −1 78413199 78444777 STUB1 −0.207566771 0.153912233 0.002187832 chr16 1 730276 732753 FUT10 −0.255860029 0.153688953 0.005536724 chr8 −1 33228342 33330664 ICMT −0.21685651 0.152232106 0.015216296 chr1 −1 6281253 6296000 LRBA −0.315333638 0.151893065 0.010448278 chr4 −1 151185811 151936649 EHMT1 −0.241468906 0.150791458 0.013619894 chr9 1 140513454 140730576 FTL −0.40992921 0.150732024 0.002344711 chr19 1 49468566 49470135 GCA −0.298984935 0.150493917 0.026770541 chr2 1 163200598 163217930 VHL −0.322679425 0.150010619 0.048079287 chr3 1 10182692 10193904 C20orf11 −0.245288407 0.14936575 0.00821144 chr20 1 61569471 61576996 GLE1 −0.21471907 0.147240709 0.033090498 chr9 1 131266979 131304567 ZMYND10 −0.292895152 0.146712105 0.026612085 chr3 −1 50378541 50384283 UTP23 −0.374374515 0.146611717 0.013067857 chr8 1 117778742 117786923 ZNF800 −0.328840317 0.146273616 0.040079467 chr7 −1 127010097 127032745 ANAPC16 −0.236656505 0.146205702 0.000286552 chr10 1 73975806 73993587 CCDC101 −0.379871865 0.14603909 0.007688959 chr16 1 28565247 28603111 LSM1 −0.36579053 0.145809293 0.002659766 chr8 −1 38020861 38034026 ZXDC −0.388243791 0.145399232 0.016752984 chr3 −1 126156444 126194762 CISH −0.274974325 0.145147773 0.017359591 chr3 −1 50643927 50649203 MAP2K7 −0.239304567 0.144528938 0.025928281 chr19 1 7968776 7979363 RPS13 −0.37147841 0.144381377 1.10E−05 chr11 −1 17095939 17099220 MSH3 −0.33197287 0.143517844 0.015896109 chr5 1 79950467 80172279 NFX1 −0.284450733 0.143446264 0.014695532 chr9 1 33290509 33371155 TM7SF3 −0.281259298 0.143055372 0.043963475 chr12 −1 27124519 27167339 SSNA1 −0.294481831 0.142992315 0.003593741 chr9 1 140083099 140084822 JAG1 −0.207653553 0.141910631 0.038493212 chr20 −1 10618332 10654608 RFESD −0.334412968 0.138496486 0.042433641 chr5 1 94982458 94991894 RPRD2 −0.324095455 0.138444802 0.032478704 chr1 1 150337126 150449042 GSTK1 −0.308788461 0.138131347 0.014538232 chr7 1 142960522 142966088 SNORD118 −0.269386914 0.137651173 0.04365142 chr17 −1 8076296 8079714 TGM2 −0.299628157 0.136635576 0.046681146 chr20 −1 36756863 36793774 PDDC1 −0.34266226 0.135701804 0.01059529 chr11 −1 767225 777484 E2F1 −0.257226115 0.134080862 0.014042676 chr20 −1 32263489 32274210 FKBP15 −0.234494526 0.133751679 0.001575025 chr9 −1 115923286 115983598 ZNF839 −0.338895641 0.13254872 0.027084505 chr14 1 102786096 102809044 ACOX3 −0.315455915 0.130554453 0.031006081 chr4 −1 8368439 8442450 LYPLA2 −0.248433242 0.129501428 0.012651101 chr1 1 24117460 24122029 ZC3H4 −0.517757699 0.129458801 0.020656821 chr19 −1 47567449 47617009 TRIM41 −0.225225314 0.129032229 0.048659242 chr5 1 180650290 180662808 NDUFB2 −0.284421962 0.128404241 0.014881978 chr7 1 140396471 140422590 CYB561D2 −0.306400325 0.12830587 0.019098432 chr3 1 50388126 50391500 HNRNPH3 −0.364665187 0.127667928 0.042931425 chr10 1 70091832 70102944 MBLAC1 −0.260766689 0.126590252 0.030855091 chr7 1 99724317 99726118 C11orf68 −0.304144949 0.125480629 0.018923113 chr11 −1 65684281 65686531 STUB1 −0.207566771 0.12452866 0.013277159 chr16 1 730276 732753 GTF2B −0.312543543 0.124424797 0.03431258 chr1 −1 89318615 89357301 −0.225423721 0.12416237 0.006205245 chr6 1 31939608 31949228 UBR3 −0.344642797 0.124057629 0.001866437 chr2 1 170684018 170940637 IQCK −0.272202349 0.123469882 0.04078684 chr16 1 19727778 19868907 RANBP10 −0.315427602 0.123149588 0.020181357 chr16 −1 67757005 67840555 CAPN1 −0.371381368 0.12269716 0.049861321 chr11 1 64949343 64979476 EFR3A −0.329905044 0.12192648 0.045753502 chr8 1 132916335 133025889 TATDN2 −0.281563426 0.120041142 0.010070144 chr3 1 10289707 10322900 ADIPOR1 −0.222354088 0.119248118 0.008669656 chr1 −1 202909951 202927517 SLC48A1 −0.243259292 0.118141827 0.049293803 chr12 1 48166991 48176536 C2CD3 −0.304566241 0.117898755 0.02071424 chr11 −1 73724430 73882064 POLR2L −0.32790758 0.117102078 0.027745289 chr11 −1 839721 842545 SLC38A7 −0.287708322 0.115656321 0.035591081 chr16 −1 58699013 58718674 ZNF697 −0.285615275 0.114911371 0.027013127 chr1 −1 120162000 120190390 USP4 −0.220679768 0.114459518 0.023789104 chr3 −1 49315264 49377466 −0.340034255 0.112566416 0.007423627 chr1 −1 247150269 247171210 NDUFB2 −0.284421962 0.112507547 0.034290656 chr7 1 140396471 140422590 RRAGA −0.378924933 0.111128217 0.01910305 chr9 1 19049372 19051019 FAM161A −0.256344752 0.11046809 0.002229884 chr2 −1 62051991 62081278 ANGEL2 −0.386058099 0.110047064 0.012069939 chr1 −1 213180327 213189168 RAD18 −0.294092376 0.109844952 0.025671988 chr3 −1 8918760 9005186 FBXO31 −0.338742144 0.10983136 0.036850372 chr16 −1 87362944 87417394 TATDN2 −0.281563426 0.109762843 0.033195763 chr3 1 10289707 10322900 DNAJC9 −0.362712454 0.109400292 0.039051442 chr10 −1 75002582 75008620 RNF181 −0.293406944 0.109205066 0.015530169 chr2 1 85822857 85824704 PXMP2 −0.249805307 0.108969797 0.02925455 chr12 1 133287436 133295746 COPE −0.343473643 0.10818861 0.043136212 chr19 −1 19010323 19030199 RPL41 −0.279151527 0.107417407 5.80E−05 chr12 1 56510572 56511308 WHSC2 −0.329016517 0.105970321 0.015863743 chr4 −1 1984441 2011837 TMED2 −0.238864154 0.105035201 0.015444836 chr12 1 124069076 124082681 RPS28 −0.252441473 0.104337089 0.006397904 chr19 1 8386384 8387278 TRPC4AP −0.420345973 0.103761538 0.021125114 chr20 −1 33590207 33680674 C1orf56 −0.421783765 0.103495874 0.036623214 chr1 1 151020216 151023896 CCDC101 −0.379871865 0.100050955 0.030767786 chr16 1 28565247 28603111 FKBP15 −0.234494526 0.099742471 0.013493827 chr9 −1 115923286 115983598 C19orf55 −0.265538386 0.099394395 0.016475512 chr19 1 36249117 36259447 SLC39A1 −0.249518474 0.099224424 0.047311692 chr1 −1 153931575 153936048 C3orf1 −0.256014544 0.098068182 0.028620778 chr3 1 119217379 119243937 ZNF410 −0.212557239 0.097841091 0.0229483 chr14 1 74353574 74398980 RANGRF −0.256581556 0.097053625 0.0429601 chr17 1 8191989 8192904 RPTOR −0.322737642 0.096188417 0.038807285 chr17 1 78518625 78940173 HARBI1 −0.228571217 0.09522732 0.023940738 chr11 −1 46624411 46638777 FAM192A −0.291697248 0.095171857 0.028782031 chr16 −1 57186387 57219976 RABEPK −0.32443941 0.090453228 0.022127909 chr9 1 127962824 127984666 MORF4 −0.367250341 0.089105317 0.042713428 chr15 1 79165211 79190475 ARMC2 −0.325357455 0.080694621 0.035527188 chr6 1 109169625 109295186 UBAP1 −0.27003315 0.075360164 0.039322863 chr9 1 34179011 34252521 KIAA1430 −0.230619058 0.073236235 0.036554003 chr4 −1 186090180 186125182 SNORD73A −0.245144596 0.070121069 0.008430314 chr4 1 152020725 152025804 EIF4G2 −0.261394891 0.070102425 0.032635321 chr11 −1 10818593 10830017 SNORD73A −0.245144596 0.063919673 0.04188973 chr4 1 152020725 152025804 SNORD73A −0.245144596 0.063555007 0.015705811 chr4 1 152020725 152025804 geneName affyid DMRstart DMRend Distance To TSS QPCT 205174_s_at 37571717 37571717 −261 ANLN 222608_s_at 36429415 36429415 −759 SLC6A6 228754_at 14444076 14444076 −590 CEP55 218542_at 95256389 95256389 509 ANLN 1552619_a_at 36429415 36429415 −759 TGFBI 201506_at 135364584 135364584 548 ME1 204058_at 84140790 84140790 −757 TRIP13 204033_at 892758 892758 −743 CTPS 202613_at 41445007 41445007 1600 ME1 204059_s_at 84140790 84140790 −757 HELLS 223556_at 96305574 96305574 −1367 CCNB1 228729_at 68462837 68462837 1104 MET 203510_at 116312446 116312446 −950 TRIP6 209129_at 100464760 100464760 −1046 202357_s_at 31913486 31913486 693 IL20RA 219115_s_at 137366101 137366101 −235 TTK 204822_at 80714322 80714322 −1083 CDK1 203213_at 62538212 62538212 1643 PRC1 218009_s_at 91537749 91537749 −939 CCNB1 214710_s_at 68462837 68462837 1104 CDCA2 226661_at 25316513 25316513 1442 ARG2 203946_s_at 68086579 68086579 −1290 PHF19 227212_s_at 123639606 123639606 1550 SLC6A6 205920_at 14444076 14444076 −590 TK1 1554408_a_at 76183314 76183314 −443 CDK1 210559_s_at 62538212 62538212 1643 C12orf48 227928_at 102513956 102513956 −822 LRRC6 206483_at 133687813 133687813 953 CDKN3 1555758_a_at 54863673 54863673 1205 MET 213816_s_at 116312446 116312446 −950 CDKN3 209714_s_at 54863673 54863673 1205 ITGA2 227314_at 52285156 52285156 −1396 GART 217445_s_at 34915148 34915148 1539 KPNA2 211762_s_at 66031848 66031848 −926 MET 213807_x_at 116312446 116312446 −950 FAM57A 218898_at 635798 635798 1089 CDK1 203214_x_at 62538212 62538212 1643 GPT2 224839_s_at 46918290 46918290 868 PDCD2L 224467_s_at 34895303 34895303 −511 C12orf48 220060_s_at 102513956 102513956 −822 SLC39A10 225295_at 196521471 196521471 −365 HOXB6 205366_s_at 46682354 46682354 −426 MET 211599_x_at 116312446 116312446 −950 DHFRP1 202533_s_at 79950802 79950802 −784 222757_s_at 173940442 173940442 1785 ERO1L 222646_s_at 53162423 53162423 1515 FERMT1 218796_at 6104191 6104191 −318 MOCOS 219959_at 33767482 33767482 708 GART 212378_at 34915148 34915148 1539 FERMT1 60474_at 6104191 6104191 −318 C1orf59 225841_at 109204148 109204148 −200 CENPH 231772_x_at 68485375 68485375 −859 RUVBL1 201614_s_at 127842667 127842667 −439 FBXO5 218875_s_at 153304153 153304153 1194 SPNS2 225671_at 4402129 4402129 1848 SLC22A3 205421_at 160769300 160769300 1247 SCD 211708_s_at 102106877 102106877 981 C13orf37 225578_at 73301825 73301825 −1370 TK1 202338_at 76183314 76183314 −443 ODC1 200790_at 10588630 10588630 1291 PLK4 204887_s_at 128802016 128802016 −580 BYSL 203612_at 41888926 41888926 −1093 ASPM 219918_s_at 197115824 197115824 1628 FERMT1 229545_at 6104191 6104191 −318 GMDS 204875_s_at 2245915 2245915 1328 SHMT2 214437_s_at 57623519 57623519 1011 C7orf68 1554452_a_at 128095903 128095903 1102 C7orf68 218507_at 128095903 128095903 1102 GMDS 214106_s_at 2245915 2245915 1328 TIMELESS 203046_s_at 56843200 56843200 −562 KPNA2 201088_at 66031848 66031848 −926 RAB23 220955_x_at 57086205 57086205 579 AURKA 208079_s_at 54967261 54967261 1023 TACC3 218308_at 1723266 1723266 1005 SQLE 213562_s_at 126010720 126010720 1102 NUP37 218622_at 102512361 102512361 −525 CTHRC1 225681_at 104383743 104383743 −1092 RTEL1 206467_x_at 62290756 62290756 0 NUFIP1 205135_s_at 45563618 45563618 827 PLK1 202240_at 23690143 23690143 1313 C12orf29 228378_at 88429290 88429290 −396 CEP76 52285_f_at 12702773 12702773 968 DTYMK 1553984_s_at 242626406 242626406 −1460 PHF19 227211_at 123639466 123639466 1410 RAD18 224200_s_at 9005186 9005186 −1043 SCD 200832_s_at 102106881 102106881 977 RAB23 223463_at 57087078 57087078 1452 YAP1 213342_at 101981210 101981210 −875 GSTP1 200824_at 67351066 67351066 −740 NOLC1 205895_s_at 103912117 103912117 −513 DTYMK 203270_at 242626406 242626406 −1460 PLEK2 218644_at 67878828 67878828 −490 SHMT2 214096_s_at 57623519 57623519 1011 CEP76 219311_at 12702773 12702773 968 PLK4 204886_at 128802016 128802016 −580 JAG1 209098_s_at 10654608 10654608 −1306 PKM2 201251_at 72523328 72523328 −1684 NKD1 229481_at 50582241 50582241 965 AURKA 204092_s_at 54967261 54967261 1023 FGGY 219718_at 59762663 59762663 −1010 SHMT2 214095_at 57623519 57623519 1011 FBXO22OS 225736_at 76196200 76196200 1253 SNORD118 224496_s_at 8079714 8079714 −807 DPCD 1553976_a_at 103348045 103348045 822 AHCY 200903_s_at 32891154 32891154 912 FZD6 203987_at 104311100 104311100 885 CDCA2 236957_at 25316513 25316513 1442 WARS2 218766_s_at 119683271 119683271 −673 MTHFD2 201761_at 74425689 74425689 −358 PGM2L1 229553_at 74109502 74109502 −956 WDHD1 204728_s_at 55493795 55493795 859 FHL2 202949_s_at 106016124 106016124 1979 PGM2L1 229256_at 74109502 74109502 −956 FBXO5 234863_x_at 153304153 153304153 1194 SQLE 209218_at 126010720 126010720 1102 IL20RA 222829_s_at 137366101 137366101 −235 FASN 212218_s_at 80056106 80056106 −1406 ABHD2 228490_at 89631405 89631405 1331 KIAA1704 220171_x_at 45563687 45563687 −896 GART 212379_at 34915148 34915148 1539 NOLC1 211949_s_at 103912117 103912117 −513 FBXO22OS 225737_s_at 76196200 76196200 1253 223519_at 173940570 173940570 1657 VANGL1 219330_at 116184612 116184612 −470 IMMP2L 227153_at 111202347 111202347 −661 NKD1 1553115_at 50582241 50582241 965 ZYX 200808_s_at 143078173 143078173 −1292 ABHD2 205566_at 89631405 89631405 1331 FBXO22OS 225734_at 76196200 76196200 1253 ENAH 222433_at 225840844 225840844 −1432 INCENP 242787_at 61891445 61891445 1307 LACTB2 222714_s_at 71581447 71581447 1093 ALDH7A1 208950_s_at 125931110 125931110 1325 ITGA2 205032_at 52285156 52285156 −1396 SCD 211162_x_at 102106881 102106881 977 DHFRP1 48808_at 79950802 79950802 −784 BAX 211833_s_at 49458134 49458134 −627 LACTB2 218701_at 71581447 71581447 1093 MRPS17 218982_s_at 56019512 56019512 −841 ENO1 217294_s_at 8938749 8938749 1328 C12orf5 219099_at 4430359 4430359 1093 ERCC8 1554883_a_at 60240878 60240878 840 PGD 201118_at 10459137 10459137 1096 IPO7 200994_at 9406169 9406169 −285 RPP25 219143_s_at 75249775 75249775 1379 NUP35 225470_at 183989083 183989083 −741 FAM175A 233543_s_at 84406334 84406334 984 PHLDA2 209803_s_at 2950685 2950685 1320 MEST 202016_at 130126046 130126046 −282 NOP58 223096_at 203130439 203130439 −1051 GLRX3 209080_x_at 131934663 131934663 −508 C1orf135 220011_at 26185903 26185903 767 C17orf75 203830_at 30669189 30669189 −640 IPO7 200992_at 9406169 9406169 −285 XPO5 223057_s_at 43543812 43543812 −964 YAP1 224894_at 101981210 101981210 −875 WARS2 222734_at 119683271 119683271 −673 DUS4L 205761_s_at 107204403 107204403 850 ERO1L 218498_s_at 53162423 53162423 1515 NANP 228073_at 25604811 25604811 1323 DNAJC2 213097_s_at 102985113 102985113 −438 XPO5 223055_s_at 43543812 43543812 −964 NOLC1 211951_at 103912117 103912117 −513 PPAP2C 209529_at 291435 291435 1840 HSPD1 200806_s_at 198364771 198364771 −1677 225662_at 173940570 173940570 1657 EPT1 1555274_a_at 26568982 26568982 −1458 C14orf126 1553801_a_at 31926670 31926670 960 GNPNAT1 225853_at 53258319 53258319 1066 PDXK 202671_s_at 45138978 45138978 1446 EPHA1 205977_s_at 143105985 143105985 673 225665_at 173940570 173940570 1657 L2HGDH 224460_s_at 50778947 50778947 1023 PTPLAD1 217777_s_at 65822825 65822825 −469 TOMM34 201870_at 43589127 43589127 1241 CTSH 202295_s_at 79237433 79237433 −720 PUS1 218670_at 132413813 132413813 −920 RSL1D1 212018_s_at 11945442 11945442 −726 TBC1D7 223461_at 13328763 13328763 −746 TIMM50 224913_s_at 39971052 39971052 −231 MCFD2 212246_at 47143007 47143007 1226 DNAJC9 213088_s_at 75008620 75008620 202 TBRG4 220789_s_at 45151317 45151317 1314 ALDH7A1 208951_at 125931110 125931110 1325 GCSH 213129_s_at 81130008 81130008 −565 CAMSAP1 212711_at 138799070 138799070 1398 JAG1 216268_s_at 10654608 10654608 −1306 CDK7 211297_s_at 68530700 68530700 924 NSUN4 226351_at 46805849 46805849 −515 IPO7 200993_at 9406169 9406169 −285 TROAP 1568596_a_at 49716971 49716971 −700 ZMYND19 227477_at 140484942 140484942 1064 C1orf135 222946_s_at 26185903 26185903 767 GEMIN5 225712_at 154317769 154317769 −395 MKLN1 204423_at 131012619 131012619 −1092 SHB 1557458_s_at 38069208 38069208 −1133 SKA2 225686_at 57232800 57232800 1693 TNFRSF10A 231775_at 23082639 23082639 −806 CKLF 221058_s_at 66586470 66586470 1622 CKS1B 201897_s_at 154947159 154947159 1810 NDUFAF2 228355_s_at 60240956 60240956 −918 PTPLAD1 222404_x_at 65822825 65822825 −469 PDXK 218018_at 45138978 45138978 1446 RFWD3 218564_at 74700779 74700779 −1051 ZC3H8 223506_at 113012688 113012688 950 NUBPL 220176_at 32030591 32030591 −541 ENAH 217820_s_at 225840844 225840844 −1432 DDX56 217754_at 44613601 44613601 960 VANGL1 229997_at 116184612 116184612 −470 UCHL3 204616_at 76123927 76123927 −675 ICA1 210547_x_at 8301911 8301911 −817 C5orf34 229886_at 43515247 43515247 1218 POLH 1557701_s_at 43543887 43543887 889 JAG1 209099_x_at 10654608 10654608 −1306 IPO7 200995_at 9406169 9406169 −285 ACP1 201629_s_at 264872 264872 1366 CCT4 200877_at 62115939 62115939 −465 WEE1 212533_at 9595430 9595430 −1298 HIBADH 231955_s_at 27702614 27702614 −653 YAP1 224895_at 101981210 101981210 −875 DHFRP1 202534_x_at 79950802 79950802 −784 FAM161A 242584_at 62081278 62081278 938 EXOC6 233924_s_at 94608277 94608277 −1158 NUFIP1 205134_s_at 45563618 45563618 827 PTPLAD1 234000_s_at 65822825 65822825 −469 ST7OT3 207871_s_at 116593396 116593396 −658 GART 210005_at 34914420 34914420 811 GTF3C3 218343_s_at 197664425 197664425 −726 FAM128A 213166_x_at 132249995 132249995 −1687 ICA1 207949_s_at 8301911 8301911 −817 BAX 208478_s_at 49458134 49458134 −627 ENO1 201231_s_at 8938749 8938749 1328 SUSD1 226264_at 114937465 114937465 −827 SKIL 217591_at 170077411 170077411 −435 SLC6A6 205921_s_at 14444076 14444076 −590 UBE3C 1554794_a_at 156931607 156931607 1361 MTHFD2 234976_x_at 74425689 74425689 −358 METTL5 221570_s_at 170681424 170681424 −814 C7orf44 209445_x_at 43769088 43769088 −1021 NAA38 219119_at 117824086 117824086 −992 PSMDI2 202352_s_at 65362743 65362743 1176 UBA2 201177_s_at 34919268 34919268 −531 INTS2 224308_s_at 60005377 60005377 −492 SCD 200831_s_at 102106881 102106881 977 ZYX 215706_x_at 143078173 143078173 −1292 C12orf45 226349_at 105380098 105380098 −475 PHF19 225533_at 123639606 123639606 1550 PTPLAD1 222405_at 65822825 65822825 −469 CCT8 200873_s_at 30446118 30446118 1632 GTPBP10 234311_s_at 89975979 89975979 −1015 POLR3K 218866_s_at 103628 103628 1047 ZNF200 207338_s_at 3285175 3285175 −806 DCLRE1A 209804_at 115614142 115614142 761 CSTF3 229666_s_at 33183037 33183037 1661 CKLF 219161_s_at 66586470 66586470 1622 MAP3K8 205027_s_at 30722866 30722866 −1094 C12orf29 213701_at 88429290 88429290 −396 POLR1D 218258_at 28194903 28194903 −1553 218833_at 173940687 173940687 1540 C14orf126 227158_at 31926670 31926670 960 DHFRP1 202532_s_at 79950802 79950802 −784 CCT5 208696_at 10250033 10250033 1696 POLH 222879_s_at 43543887 43543887 889 FPGS 202945_at 130565154 130565154 1051 GCSH 213133_s_at 81130008 81130008 −565 ATP5S 213995_at 50779047 50779047 −1123 THEM4 229253_at 151882284 151882284 −463 VANGL1 229492_at 116184612 116184612 −470 GSG2 223759_s_at 3627197 3627197 996 PXMP2 1555943_at 133287436 133287436 888 CAMSAP1 212712_at 138799070 138799070 1398 ORMDL2 218556_at 56211806 56211806 844 C16orf55 230811_at 89724152 89724152 1235 ABHD2 87100_at 89631405 89631405 1331 ABHD2 63825_at 89631405 89631405 1331 MRPS28 219819_s_at 80942506 80942506 −841 KDM1A 212348_s_at 23345941 23345941 −696 PDCD11 212422_at 105156405 105156405 −1019 C17orf79 225096_at 30186256 30186256 −488 WEE1 215711_s_at 9595430 9595430 −1298 PDF 219575_s_at 69373513 69373513 −1151 LRSAM1 235449_at 130213784 130213784 1092 TNFRSF10A 1552648_a_at 23082639 23082639 −806 C16orf88 213237_at 19726362 19726362 −780 PLK4 211088_s_at 128802016 128802016 −580 DPCD 226009_at 103348045 103348045 822 KIAA0895 213424_at 36429734 36429734 1078 DDX55 231843_at 124086672 124086672 −883 GPHN 220773_s_at 66974125 66974125 −640 WDR36 238677_at 110427414 110427414 −60 CKLF 223451_s_at 66586470 66586470 1622 SRD5A1 210959_s_at 6633456 6633456 −1370 C6orf223 230944_at 43968337 43968337 0 WDHD1 216228_s_at 55493795 55493795 859 SRD5A1 204675_at 6633456 6633456 −1370 227805_at 172864490 172864490 −217 CSNK1E 225756_at 38714089 38714089 −539 UCHL5 220083_x_at 193028539 193028539 1268 HSPD1 200807_s_at 198364771 198364771 −1677 SNORD118 239824_s_at 8079714 8079714 −807 RANGRF 218526_s_at 8191989 8191989 −832 OAS3 218400_at 113376157 113376157 1319 EEPD1 225631_at 36192758 36192758 −746 AARSD1 222064_s_at 41132020 41132020 347 PRPF19 203103_s_at 60674056 60674056 −990 ACP1 215227_x_at 264869 264869 1369 RAB23 229504_at 57087078 57087078 1452 GALK2 205219_s_at 49447976 49447976 −1441 BBS2 223227_at 56554195 56554195 1252 SHB 204657_a_at 38069208 38069208 −1133 TALDO1 201463_s_at 747329 747329 1421 SLC27A2 205769_at 50474394 50474394 1333 XPO5 223056_s_at 43543812 43543812 −964 SNORD118 238590_x_at 8079714 8079714 −807 SLC27A2 205708_s_at 50474394 50474394 1333 CENPO 226118_at 25016014 25016014 −846 DBR1 234295_at 137893791 137893791 1138 TUBGCP4 211337_s_at 43663293 43663293 948 PSMC3IP 213951_s_at 40729747 40729747 828 GTF3C3 222604_at 197664425 197664425 −726 PCBD2 1554894_a_at 134240596 134240596 1333 CSNK1E 222015_at 38713413 38713413 −1215 DAK 218688_at 61100654 61100654 812 SKIL 206675_s_at 170075514 170075514 1147 MMACHC 211774_s_at 45965725 45965725 1200 HSPE1 205133_s_at 198364718 198364718 1730 HNRNPD 209330_s_at 83295109 83295109 −1616 EEPD1 225630_at 36192758 36192758 −746 KARS 200840_at 75681577 75681577 862 NMI 203964_at 152146571 152146571 1086 CSTF3 203947_at 33183037 33183037 1661 PLBD1 218454_at 14720791 14720791 −595 TUBA4A 212242_at 220118754 220118754 1937 ANAPC7 225521_at 110841535 110841535 −710 RABEPK 203150_at 127962882 127962882 −975 USP18 219211_at 18632666 18632666 784 CSTF1 202190_at 54967450 54967450 −1212 SRPK2 1558254_s_at 105029341 105029341 −807 GPHN 223319_at 66974125 66974125 −640 RAB15 59697_at 65438875 65438875 −810 SLC48A1 218417_s_at 48166991 48166991 −497 PHB 200658_s_at 47492242 47492242 −1192 GLRX3 214205_x_at 131934663 131934663 −508 THEM4 243492_at 151882284 151882284 −463 PSMC2 201068_s_at 102985361 102985361 190 RAD18 223417_at 9005186 9005186 −1043 ASPSCR1 218908_at 79935426 79935426 1014 FLVCR1 222906_at 213031597 213031597 917 PDCD11 212424_at 105156405 105156405 −1019 C13orf34 219544_at 73302064 73302064 1131 SDCCAG3 218427_at 139305061 139305061 −1069 CAMSAP1 212710_at 138799070 138799070 1398 HIBADH 224812_at 27702614 27702614 −653 SNORD118 224495_at 8079714 8079714 −807 SHB 204656_at 38069208 38069208 −1133 SPC24 235572_at 11266458 11266458 656 PSMD1 201198_s_at 231921578 231921578 1189 KIAA0319 206017_at 24646383 24646383 −692 AARS 201000_at 70323409 70323409 1250 THEM4 1553118_at 151882284 151882284 −463 KIAA1324 243349_at 109656729 109656729 −1672 PERP 222392_x_at 138428648 138428648 1690 PPP2R1B 202884_s_at 111637169 111637169 −996 SAAL1 225614_at 18127638 18127638 −488 BLVRA 203771_s_at 43798279 43798279 917 WDR5B 219538_at 122134882 122134882 −1127 MAP7 202889_x_at 136871646 136871646 −774 KARS 200079_s_at 75681577 75681577 862 G2E3 223255_at 31028364 31028364 −885 RAB15 221810_at 65438875 65438875 −810 COPS2 202467_s_at 49447854 49447854 1319 JHDM1D 225142_at 139876835 139876835 −1311 TNFRSF10A 241371_at 23082639 23082639 −806 PERP 217744_s_at 138428648 138428648 1690 CCDC77 224521_s_at 510742 510742 −561 DAP3 208822_s_at 155658849 155658849 933 ZNF643 207219_at 40916716 40916716 −1567 ABHD2 221815_at 89631405 89631405 1331 NSUN2 223076_s_at 6633404 6633404 1318 LRRC2 219949_at 46608040 46608040 −234 TARS 201263_at 33440802 33440802 1714 HSPD1 243372_at 198364771 198364771 −1677 UBXN10 238657_a1 20512578 20512578 −390 KLHDC5 225963_at 27933187 27933187 −852 MRPL16 217980_s_at 59578345 59578345 1074 TGEBR2 207334_s_at 30647994 30647994 1908 F3 204363_at 95007356 95007356 793 G2E3 223257_at 31028364 31028364 −885 G2E3 223258_s_at 31028364 31028364 −885 SLC48A1 48106_at 48166991 48166991 −497 BLVRA 203773_x_at 43798279 43798279 917 C2orf15 243887_at 99797542 99797542 1120 PGM2L1 238417_at 74109502 74109502 −956 MAP7 215471_s_at 136871646 136871646 −774 WDR36 226180_at 110427414 110427414 −60 UBE3C 201817_4 156931607 156931607 1361 G2E3 223254_s_at 31028364 31028364 −885 POLQ 219510_at 121264853 121264853 −1103 RIF1 214700_x_at 152266397 152266397 −340 SLC2A8 218985_at 130159421 130159421 −1131 IDE 217496_s_at 94333833 94333833 1275 IDE 203328_x_at 94333833 94333833 1275 FAM175A 226521_s_at 84406334 84406334 984 ADRM1 201281_at 60878061 60878061 1209 SMPD4 207856_s_at 130939166 130939166 948 MSH3 210947_s_at 79950467 79950467 1119 NENF 214075_at 212606229 212606229 −956 ESF1 222765_x_at 13765532 13765532 −1474 RNMTL1 218993_at 685513 685513 −924 NAA16 1555450_a_at 41885341 41885341 −391 TROAP 204649_at 49716971 49716971 −700 DDX50 221699_s_at 70661034 70661034 −651 POLH 233852_at 43543887 43543887 889 CEP57 203491_s_at 95523642 95523642 1256 SQLE 213577_at 126010720 126010720 1102 HNRNPA3 211931_s_at 178077291 178077291 −994 SERBP1 209669_a_at 67896098 67896098 −1338 PATL1 235234_at 59436511 59436511 −1162 NARF 219862_s_at 80416540 80416540 −923 UTP23 238562_at 117778742 117778742 −638 EIF2A 223015_at 150264481 150264481 1080 DNAJC15 218435_at 43597339 43597339 −76 CCIAD2 225314_at 48908845 48908845 945 GLS2 205531_s_at 56882181 56882181 1060 EXTL2 209537_at 101361554 101361554 −1140 NIP7 223397_s_at 69373343 69373343 1321 ERGIC2 226422_at 29534143 29534143 −582 GNPDA1 202382_s_at 141392596 141392596 −675 NIP7 219031_s_at 69373343 69373343 1321 ACLY 210337_s_at 40075240 40075240 −972 C19orf20 227903_x_at 507497 507497 1231 CARS2 218153_at 111358485 111358485 853 DEAF1 209407_s_at 695047 695047 −1744 PYCRL 218944_at 144691784 144691784 −889 NCBP2 201521_s_at 196669468 196669468 −1003 EXOC6 226259_at 94608277 94608277 −1158 MIOS 206800_s_at 7606503 7606503 −604 PMPCA 212088_at 139305112 139305112 1018 FAM188B 1557141_at 30811033 30811033 −594 RPL12 200088_x_at 130213684 130213684 −1192 ABHD2 225337_at 89631405 89631405 1331 ERCC8 205162_at 60240878 60240878 840 EIF3G 208887_at 10230599 10230599 −629 RPL12 214271_x_at 130213684 130213684 −1192 FUT10 235472_at 33330664 33330664 1935 SARNP 224914_s_at 56211540 56211540 −1110 RNF24 204669_s_at 3996036 3996036 −735 NENF 218407_x_at 212606229 212606229 −956 HSD3B7 222817_at 30996532 30996532 453 FAT1 201579_at 187645009 187645009 1722 PATL1 235235_s_at 59436511 59436511 −1162 PATL1 225468_at 59436511 59436511 −1162 MYO6 210480_s_at 76458926 76458926 1177 RNF24 204668_at 3996036 3996036 −735 EBPL 223306_at 50265611 50265611 −380 SAR1A 201543_s_at 71930279 71930279 −694 RPL12 200809_x_at 130213684 130213684 −1192 RWDD2B 218377_s_at 30391699 30391699 −448 HMGCS1 205822_s_at 43313595 43313595 1163 DHX30 204355_at 47844418 47844418 −1025 TGFBR2 208944_at 30647994 30647994 1908 PCYT2 209577_at 79869294 79869294 1154 DPY19L4 213391_at 95732103 95732103 −944 METFL13 206468_s_at 171750822 171750822 1069 ANGEL2 221826_at 213189168 213189168 −548 SNRNP70 201221_s_at 49588465 49588465 −695 HNRNPU 200593_s_at 245027844 245027844 −606 MYEOV 227342_s_at 69061622 69061622 0 GLS 223079_s_at 191745560 191745560 −1119 NUFIP1 205136_s_at 45563618 45563618 827 QRSL1 218949_s_at 107077453 107077453 −1333 WHSC2 203112_s_at 2011837 2011837 −276 IFT122 220744_s_at 129158968 129158968 −1267 PSMC6 201699_at 53173890 53173890 1313 STAT1 209969_s_at 191878894 191878894 1156 PSMD1 201199_s_at 231921578 231921578 1189 SRPK2 230091_at 105029341 105029341 −807 PSMD4 210460_s_at 151227179 151227179 1258 FBXO45 225099_at 196295559 196295559 −966 ANAPC7 225554_s_at 110841535 110841535 −710 PDXK 222492_at 45138978 45138978 1446 TWSG1 219201_s_at 9334765 9334765 −994 DHX30 212674_s_at 47844418 47844418 −1025 CGREF1 205937_at 27341971 27341971 −400 LRSAM1 227675_at 130213784 130213784 1092 VPS13C 218396_at 62352672 62352672 −1090 RBM33 1554095_at 155437145 155437145 1819 CEP57 203493_s_at 95523642 95523642 1256 CHAC1 219270_at 41245347 41245347 −494 METTL13 212407_at 171750822 171750822 1069 C1orf56 223459_s_at 151020216 151020216 −485 FKBP3 218003_s_at 45604522 45604522 1652 FAMI28B 212995_x_at 130939501 130939501 −1283 SNRNP25 218493_at 103010 103010 −429 PBX4 230536_at 19729725 19729725 −518 PITPNB 202522_at 28315256 28315256 1207 DDX49 210811_s_at 19030494 19030494 −1155 H2AFJ 225245_x_at 14927349 14927349 1706 WDHD1 204727_at 55493795 55493795 859 BLVRA 211729_x_at 43798279 43798279 917 COPS2 209838_at 49447854 49447854 1319 GOPC 227214_at 117923691 117923691 −918 CCT5 229068_at 10250033 10250033 1696 215982_s_at 31940069 31940069 875 GCFC1 218515_at 34144169 34144169 −1504 PSMB6 208827_at 4699439 4699439 −502 LARP4 214155_s_at 50794650 50794650 −669 RSPH1 230093_at 43916464 43916464 1001 GLS2 1564706_s_at 56882181 56882181 1060 NFYA 204109_s_at 41040684 41040684 −1704 CEP57 203492_x_at 95523642 95523642 1256 SERBP1 210466_s_at 67896098 67896098 −1338 FUBP1 203091_at 78444770 78444770 1853 METTL13 212405_s_at 171750822 171750822 1069 ERAL1 212087_s_at 27182020 27182020 −768 GCFC1 221158_at 34144169 34144169 −1504 RNF24 210706_s_at 3996036 3996036 −735 ATXN3 205415_s_at 92572954 92572954 −440 WHSC2 34225_at 2011837 2011837 −276 PSMG2 218467_at 12702425 12702425 −620 DBR1 219149_x_at 137893791 137893791 1138 TXLNA 212300_at 32645287 32645287 −508 RAGE 205130_at 102771531 102771531 −664 H2AFJ 224301_x_at 14927349 14927349 1706 CSNK1E 202332_at 38714089 38714089 −539 PSMD4 200882_s_at 151227179 151227179 1258 CCDC21 227818_at 26560693 26560693 1259 MAPKAPK3 202787_s_at 50649339 50649339 −1345 LRFN4 219491_at 66624589 66624589 575 FKTN 205283_at 108320411 108320411 −1015 SRD5A1 211056_s_at 6633456 6633456 −1370 TMCO7 226467_at 68877509 68877509 −688 MRPL15 218027_at 55047781 55047781 −526 ANKRD26 205706_s_at 27389421 27389421 −727 CENPV 226611_s_at 16256813 16256813 1476 MANIB1 65884_at 139981400 139981400 1075 GPR137B 204137_at 236305832 236305832 −1848 TUBA1B 212639_x_at 49525304 49525304 −1445 PPP2R1B 202886_s_at 111637169 111637169 −996 MYO6 203216_s_at 76458926 76458926 1177 SEC23B 201583_s_at 18488199 18488199 −604 MED1 225456_at 37607521 37607521 914 GCLC 202923_s_at 53409927 53409927 −401 G2E3 223256_at 31028364 31028364 −885 ASNA1 202024_at 12848306 12848306 −1266 FBXO45 225100_at 196295559 196295559 −966 AIDA 220199_s_at 222885866 222885866 −1619 NUP50 218295_s_at 45559722 45559722 −956 DAG1 205417_s_at 49507565 49507565 −974 WDR33 222763_s_at 128568745 128568745 1440 ATP5S 206992_s_at 50779047 50779047 −1123 SERBP1 217725_x_at 67896098 67896098 −1338 LARP4 1555384_a_at 50794650 50794650 −669 MITD1 226329_s_at 99797390 99797390 −1272 SRPK2 214931_s_at 105029341 105029341 −807 ACP1 201630_s_at 264869 264869 1369 FAM188B 235559_at 30811033 30811033 −594 UBXN10 232109_at 20512578 20512578 −390 PLOD3 202185_at 100860954 100860954 1056 XRCC6 200792_at 42017123 42017123 −1320 STARD4 226390_at 110848208 110848208 −1062 ADSS 221761_at 244615436 244615436 485 NFYA 204107_at 41040684 41040684 −1704 IDE 241300_at 94333833 94333833 1275 MAPKAPK3 202788_at 50649339 50649339 −1345 TUBA1B 213646_x_at 49525304 49525304 −1445 RTEL1 216325_x_at 62289163 62289163 1455 MIOS 211724_x_at 7606503 7606503 −604 TMEM43 222418_s_at 14166440 14166440 −1225 WDR59 221981_s_at 75019017 75019017 −403 SLC1A4 209610_s_at 65216535 65216535 1620 ERO1L 225750_at 53162423 53162423 1515 CSTF3 229665_at 33183037 33183037 1661 PNN 212037_at 39644425 39644425 −835 CEP57 209862_s_at 95523642 95523642 1256 DCTN4 218013_x_at 150138671 150138671 −363 LTA4H 208771_s_at 96429365 96429365 1334 PSMD4 211609_x_at 151227179 151227179 1258 DPY19L3 225633_at 32897031 32897031 423 USE1 219348_at 17326155 17326155 651 TFCP2 209338_at 51566664 51566664 −1168 ANXA2 213503_x_at 60690185 60690185 1563 NUP50 222583_s_at 45559722 45559722 −956 ICA1 204002_s_at 8301911 8301911 −817 209219_at 31926887 31926887 815 ANXA2 210427_x_at 60690185 60690185 1563 USE1 221706_s_at 17326155 17326155 651 TBC1D30 213912_at 65174589 65174589 −551 C17orf81 219260_s_at 7155372 7155372 1242 ANXA2 201590_x_at 60690185 60690185 1563 PSMB1 200876_s_at 170862429 170862429 1342 CAPN10 221040_at 241526189 241526189 1153 USP45 224441_s_at 99963365 99963365 1246 TUBA1B 211072_x_at 49525304 49525304 −1445 C20orf108 224693_at 54933971 54933971 −549 CREB3L2 228759_at 137686803 137686803 −850 TMEM43 217795_s_at 14166440 14166440 −1225 SETD3 212465_at 99947216 99947216 1843 SLC6A6 211030_s_at 14444120 14444120 −634 DGCR14 204383_at 19132197 19132197 −472 SRPK2 203182_s_at 105029341 105029341 −807 PGM2L1 235149_at 74109502 74109502 −956 GBAS 201816_s_at 56032274 56032274 −542 CSTF1 32723_at 54967450 54967450 −1212 RDH10 226021_at 74207265 74207265 1334 C3orf75 229863_s_at 47555251 47555251 −615 ZNF318 203521_s_at 43337181 43337181 −1063 ASPM 239002_at 197115824 197115824 1628 RB1 211540_s_at 48877911 48877911 −917 TTLL1 205652_s_at 43485434 43485434 −513 TUBA1B 201090_x_at 49525304 49525304 −1445 PARP9 223220_s_at 122283424 122283424 −885 PRPF3 202251_at 150293925 150293925 −548 VANGL1 229134_at 116184574 116184574 −432 CLTA 204050_s_at 36190920 36190920 1468 VGLL4 212399_s_at 11762220 11762220 −782 TUBA1B 211058_x_at 49525304 49525304 −1445 PYCR2 231715_s_at 226111959 226111959 −761 GPX4 201106_at 1103966 1103966 1576 GCFC1 1555125_at 34144169 34144169 −1504 MAD1L1 204857_at 2272609 2272609 −606 TCEB2 200085_s_at 2827251 2827251 1043 CLTA 200960_x_at 36190920 36190920 1468 SC4MOL 209146_at 166248775 166248775 −1105 SLC19A2 209681_at 169455241 169455241 −1326 C20orf108 224690_at 54933971 54933971 −549 C20orf7 227160_s_at 13765596 13765596 1410 ZNF318 203520_s_at 43337181 43337181 −1063 ATXN3 205416_s_at 92572954 92572954 −440 GRINL1B 212241_at 57884106 57884106 −584 NCBP1 209520_s_at 100395908 100395908 1543 FAM173B 225670_at 10249998 10249998 −1731 GTPBP10 239773_at 89975990 89975990 −1026 IQCK 213392_at 19727778 19727778 0 CLTA 216295_s_at 36190920 36190920 1468 ZMYND10 203246_s_at 50384283 50384283 619 PATL1 225466_at 59436511 59436511 −1162 CEP57 203494_s_at 95523642 95523642 1256 ZNF200 214706_at 3285175 3285175 −806 ZEP1 226807_at 75182480 75182480 836 SLC6A20 219614_s_at 45838027 45838027 751 MRPL14 225201_s_at 44095194 44095194 1437 DGCR14 32032_at 19132197 19132197 −472 DDB1 208619_at 61100666 61100666 −800 PSMC3IP 205956_x_at 40729747 40729747 828 MAP2K1 202670_at 66679155 66679155 −660 KIF20B 205235_s_at 91461367 91461367 1116 FAM161A 1557385_at 62081278 62081278 938 OXSM 219133_at 25831571 25831571 −904 TRMU 213634_s_at 46731322 46731322 −301 ILKAP 221548_s_at 239112370 239112370 1481 LRRC27 1558483_at 134145658 134145658 739 C20orf7 222894_x_at 13765596 13765596 1410 RABL3 226089_at 120461384 120461384 −1339 ACLY 201127_s_at 40075240 40075240 −972 SKA2 225684_at 57232800 57232800 1693 ZBTB5 203026_at 37465396 37465396 −1923 ATP9B 214934_at 76829397 76829397 1305 CCDC90B 218288_s_at 82997215 82997215 −621 EHMT1 225461_at 140513454 140513454 −1226 TBC1D30 213913_s_at 65174589 65174589 −551 PSMB1 214288_s_at 170862429 170862429 1342 NICN1 223442_at 49466674 49466674 792 KLC2 218906_x_at 66025190 66025190 −1370 ACLY 201128_s_at 40075240 40075240 −972 PDSS1 220865_s_at 26986588 26986588 −791 209040_s_at 32811824 32811824 991 MTCH2 217772_s_at 47664206 47664206 −740 TMEM14B 223133_at 10747973 10747973 −631 MKS1 1555820_a_at 56296666 56296666 −682 SPA17 205406_s_at 124543740 124543740 −847 DPH3 225195_at 16306479 16306479 −1321 HNRNPU 216855_s_at 245027844 245027844 −606 MYO6 203215_s_at 76458926 76458926 1177 IDE 203327_at 94333833 94333833 1275 1569029_at 172864490 172864490 −217 PNN 1567214_a_at 39644425 39644425 −835 SOCS4 1552792_at 55493948 55493948 −1012 UCHL5 219960_s_at 193028626 193028626 1355 CCDC97 235495_at 41816094 41816094 1117 CENPB 212437_at 3767337 3767337 972 BRF2 218954_s_at 37707411 37707411 −560 SNORA41 200705_s_at 207024309 207024309 −1328 ESD 209009_at 47371367 47371367 −620 BRE 211566_x_at 28113596 28113596 851 C3orf75 223277_at 47555251 47555251 −615 IWS1 224768_at 128284044 128284044 −1211 CHMP4A 218571_s_at 24683075 24683075 −971 DDX49 31807_at 19030494 19030494 −1155 U2AF2 218381_s_at 56165416 56165416 −663 FBXO22OS 219638_at 76196200 76196200 1253 HNRNPA3 211933_s_at 178077291 178077291 −994 PIP5K1A 211205_x_at 151171027 151171027 1250 ST7OT3 207524_at 116593381 116593381 −643 MAN1B1 218636_s_at 139981400 139981400 1075 PHB 200659_s_at 47492242 47492242 −1192 PTPDC1 238841_at 96793076 96793076 774 TMEM14B 221452_s_at 10747973 10747973 −631 TFCP2 207627_s_at 51566664 51566664 −1168 HNRNPU 200594_x_at 245027844 245027844 −606 TMEM18 225489_at 677439 677439 1216 RBM33 226732_at 155437373 155437373 1591 C20orf24 224376_s_at 35234137 35234137 −609 BRAP 209922_at 112123790 112123790 1022 ARL5B 242727_at 18948334 18948334 1567 ANKRD26 205705_at 27389421 27389421 −727 OSTC 223001_at 109571740 109571740 −1076 FLVCR1 228191_at 213031597 213031597 917 CHMP4A 218572_at 24683075 24683075 −971 BRE 212645_x_at 28113596 28113596 851 C20orf24 223880_x_at 35234137 35234137 −609 NFYA 204108_at 41040684 41040684 −1704 COQ7 210820_x_at 19078921 19078921 −377 ICMT 201609_x_at 6296000 6296000 1150 HTRA2 203089_s_at 74756504 74756504 −605 RDH10 1552378_s_at 74207265 74207265 1334 INCENP 219769_at 61891445 61891445 1307 PPME1 217841_s_at 73882368 73882368 1052 BAG4 219624_at 38034312 38034312 −1369 RTN4IP1 224509_s_at 107077362 107077362 1242 MED1 203497_at 37607521 37607521 914 EIF2AK4 225164_s_at 40226347 40226347 −637 LRRC61 218907_s_at 150020352 150020352 1201 ESD 215096_s_at 47371367 47371367 −620 C11orf83 229099_at 62439126 62439126 1139 SARNP 229069_at 56211540 56211540 −1110 204090_at 31939608 31939608 −414 CENPV 226610_at 16256813 16256813 1476 ESCO1 226866_at 19180845 19180845 1727 KPNA4 209653_at 160283376 160283376 −1247 238613_at 173940570 173940570 1657 ROCK2 211504_x_at 11484711 11484711 −1319 HTRA2 211152_s_at 74756504 74756504 −605 AKAP11 203156_at 42846289 42846289 −982 CCDC21 219611_s_at 26560693 26560693 1259 38157_at 31940069 31940069 875 DHX57 213420_at 39103049 39103049 −686 DNTTIP1 234942_s_at 44420576 44420576 −685 ETAA1 219216_at 67624451 67624451 1299 CNIH4 218728_s_at 224544552 224544552 1458 PRPSAP1 202529_at 74350230 74350230 −741 HEXA 201765_s_at 72668817 72668817 −332 PDSS2 1555886_at 107780768 107780768 1050 GPR19 207183_at 12849121 12849121 212 C3orf67 239697_x_at 59035810 59035810 658 BRE 205550_s_at 28113596 28113596 851 ASXL2 226251_at 26101385 26101385 −653 NHLRC2 235356_at 115614420 115614420 −1039 POLD3 212836_at 74303629 74303629 −496 TRAPPC6A 204985_s_at 45681485 45681485 −1862 C1orf56 221222_s_at 151020216 151020216 −485 RPIA 212973_at 88991162 88991162 −847 PPP2R1B 202883_s_at 111637169 111637169 −996 GPHN 234941_s_at 66974125 66974125 −640 PTPDC1 229517_at 96793076 96793076 774 MRPL49 201717_at 64889728 64889728 749 MKKS 222530_s_at 10414870 10414870 951 XYLB 208318_s_at 38388270 38388270 956 MSRB2 218773_s_at 23384435 23384435 1144 PNN 212036_s_at 39644425 39644425 −835 CTSB 200838_at 11725738 11725738 1705 CD81 200675_at 2398520 2398520 −459 SEL1L3 212314_at 25865217 25865217 −478 KPNA4 225268_at 160283376 160283376 −1247 SLC1A4 209611_s_at 65216535 65216535 1620 RASL11A 238353_at 27844464 27844464 1455 ROPN1L 223609_at 10441636 10441636 −952 PYCR2 224855_at 226111959 226111959 −761 SMAD2 203077_s_at 45456930 45456930 −1373 HNRNPD 221481_x_at 83295109 83295109 −1616 GCC1 218912_at 127225661 127225661 966 SERBP1 227369_at 67896098 67896098 −1338 ENSA 228851_s_at 150602072 150602072 −818 UTP23 227836_at 117778742 117778742 −638 ORC4L 203352_at 148778292 148778292 1406 WDR59 218505_at 75019017 75019017 −403 C20or124 217835_x_at 35234137 35234137 −609 ATP6V1H 221504_s_at 54755547 54755547 1181 STK38 202951_at 36515247 36515247 −500 SEC23B 210293_s_at 18488199 18488199 −604 SOD1 200642_at 33031935 33031935 1480 TWSG1 225406_at 9334765 9334765 −994 SDHC 202004_x_at 161284047 161284047 −554 C19orf55 1553162_x_at 36249044 36249044 873 PTOV1 212032_s_at 50354138 50354138 −456 NAA16 219378_at 41885341 41885341 −391 C5orf22 1552660_a_at 31532373 31532373 −1115 FAM76A 216897_s_at 28052490 28052490 −657 ZXDC 230106_at 126194708 126194708 −963 SLC1A4 212810_s_at 65216535 65216535 1620 LUC7L 1557067_s_at 279462 279462 −443 NCBP2 201517_at 196669468 196669468 −1003 TNFAIP8 210260_s_at 118690009 118690009 935 TMEM216 223305_at 61159865 61159865 −340 PPP5C 201979_s_at 46850294 46850294 −908 LARP4 238960_s_at 50794650 50794650 −669 HNRNPD 221480_at 83295109 83295109 −1616 FDXACB1 228817_at 111742004 111742004 −753 C1orf9 203429_s_at 172501489 172501489 −1054 PPME1 49077_at 73882368 73882368 1052 RSF1 229885_at 77531880 77531880 −1232 RFESD 239142_at 94982458 94982458 1311 ERP29 201216_at 112451152 112451152 −1174 L2HGDH 220089_at 50778947 50778947 1023 MED20 212872_s_at 41888837 41888837 1004 SRPK2 203181_x_at 105029341 105029341 −807 COMMD5 223198_x_at 146078932 146078932 −299 MKS1 218630_at 56296666 56296666 −682 NFX1 1553348_a_at 33290509 33290509 1386 C2orf60 235181_at 200820459 200820459 1282 MAP7 202890_at 136871646 136871646 −774 CMC1 228283_at 28283086 28283086 −828 FAM24B 231146_at 124639114 124639114 784 IFT88 204703_at 21141208 21141208 1019 CREB3L4 226455_at 153940379 153940379 −1532 HMGN4 202579_x_at 26538639 26538639 983 KIAA1279 212453_at 70748487 70748487 −577 ANAPC2 218555_at 140082989 140082989 −1299 UTP23 238561_s_at 117778742 117778742 −638 PIGB 242760_x_at 55611133 55611133 −503 COQ7 209746_s_at 19078921 19078921 −377 PHAX 231812_x_at 125935960 125935960 0 SLC31A1 203971_at 115983842 115983842 1129 MORN2 226790_at 39103103 39103103 632 ISOC2 218893_at 55973049 55973049 −815 PIGB 205452_at 55611133 55611133 −503 TIGD1 1553099_at 233415226 233415226 503 ZBED3 235109_at 76383148 76383148 −909 FBXO45 242294_at 196295559 196295559 −966 KIAA1704 229891_x_at 45563755 45563755 −964 DLST 215210_s_at 75348619 75348619 1043 HMOX2 218120_s_at 4526380 4526380 1160 ENSA 221487_s_at 150602053 150602053 −837 IQCE 204202_at 2598632 2598632 1165 NFX1 202585_s_at 33290509 33290509 1386 PHF5A 225309_at 41864729 41864729 763 NDUFA7 202785_at 8386280 8386280 1031 PPIL4 226472_at 149867174 149867174 −733 C2orf60 235686_at 200820459 200820459 1282 STK38 1553117_a_at 36515247 36515247 −500 ASPM 232238_at 197115824 197115824 1628 DUSP6 208893_s_at 89746296 89746296 1825 HEBP2 203430_at 138725356 138725356 −1075 HBXIP 202299_s_at 110950560 110950560 −608 GOPC 225023_at 117923691 117923691 −918 SMAD2 203076_s_at 45456930 45456930 −1373 DCTN4 222488_s_at 150138671 150138671 −363 GOPC 225022_at 117923691 117923691 −918 HEBP1 218450_at 13153221 13153221 645 PSMC2 238020_at 102985361 102985361 190 TEX264 218548_x_at 51705248 51705248 −897 NEK3 211089_s_at 52733724 52733724 −347 JOSD2 227096_at 51014477 51014477 −853 PTGES2 218083_at 130890741 130890741 −550 EPT1 224888_at 26568982 26568982 −1458 GCLC 202922_at 53409927 53409927 −401 COG5 203630_s_at 107204485 107204485 −768 PHAX 235767_x_at 125935960 125935960 0 RPL17 214291_at 47017814 47017814 309 RDH10 227467_at 74207265 74207265 1334 C20orf108 208080_at 54933971 54933971 −549 RPL36AL 207585_s_at 50087361 50087361 1082 WDR53 227814_at 196295510 196295510 917 HNRNPD 200073_s_at 83295109 83295109 −1616 ZKSCAN1 214900_at 99613204 99613204 1299 MDN1 212693_at 90529442 90529442 −1030 COMMD5 223819_x_at 146078932 146078932 −299 IQCH 224165_s_at 67547169 67547169 −1682 KIAA1704 223606_x_at 45563755 45563755 −964 RPS6KL1 223534_s_at 75389145 75389145 −225 ELL2 214446_at 95297775 95297775 −530 C4orf23 235097_at 8442532 8442532 1115 DAG1 212128_s_at 49507565 49507565 −974 DUSP6 208891_at 89746296 89746296 1825 VGLL4 214004_s_at 11762220 11762220 −782 TNFAIP8 208296_x_at 118690009 118690009 935 BAG4 228189_at 38034312 38034312 −1369 EIF4E2 213571_s_at 233414762 233414762 −39 NACAP1 200735_x_at 57119083 57119083 −707 SERBP1 217724_at 67896098 67896098 −1338 HMGN4 209786_at 26538639 26538639 983 LAP3 217933_s_at 17578815 17578815 −870 ESF1 218859_s_at 13765532 13765532 −1474 TM7SF3 222477_s_at 27167339 27167339 −778 PHAX 234405_s_at 125935960 125935960 0 AASDH 228041_at 57253666 57253666 1168 HNRNPH3 210110_x_at 70091832 70091832 −937 C17orf81 223286_at 7155372 7155372 1242 COMMD5 224387_at 146078932 146078932 −299 IQCH 239812_s_at 67547169 67547169 −1682 HN1 217755_at 73150778 73150778 1633 MED1 203496_s_at 37607521 37607521 914 WDR60 219251_s_at 158649269 158649269 −698 DCP1A 225443_at 53381637 53381637 −702 QRSL1 241933_at 107077453 107077453 −1333 ERCC3 202176_at 128051752 128051752 −581 CREB1 237289_at 208394616 208394616 −1412 IWS1 224775_at 128284044 128284044 −1211 STX10 212625_at 13261052 13261052 1180 KPNA4 225267_at 160283376 160283376 −1247 HBXIP 202300_at 110950560 110950560 −608 UNC93B1 225869_s_at 67771593 67771593 −625 SIK2 223430_at 111473192 111473192 −902 IQCH 220361_at 67547169 67547169 −1682 POLL 221049_s_at 103347966 103347966 −901 SPATA13 225564_at 24734887 24734887 −548 PSMD12 202353_s_at 65362743 65362743 1176 TMEM18 225487_at 677439 677439 1216 FAM76B 1553750_a_at 95522954 95522954 −1944 HNRNPA3 211932_at 178077477 178077477 −1180 NDUFS8 203189_s_at 67798094 67798094 −806 UBA52 221700_s_at 18682614 18682614 −756 TM7SF3 226478_at 27167339 27167339 −778 RTN4IP1 1555679_a_at 107077362 107077362 1242 SPATA13 1557470_at 24734861 24734861 −522 RIF1 226503_at 152266455 152266455 −398 ZNF428 215429_s_at 44124006 44124006 −718 EIF4E2 209393_s_at 233414762 233414762 −39 SEL1L3 212311_at 25865217 25865217 −478 MIB2 228261_at 1550884 1550884 1336 PDXK 218019_s_at 45138978 45138978 1446 NACAP1 208635_x_at 57119083 57119083 −707 NDUFS8 203190_at 67798094 67798094 −806 CBLL1 220018_at 107384142 107384142 −811 LRRC2 231781_s_at 46608040 46608040 −234 IQCE 217124_at 2598632 2598632 1165 MOCOS 238576_at 33767482 33767482 708 RTEL1 211526_s_at 62289163 62289163 1455 203727_at 31926857 31926857 −785 POLR2L 211730_s_at 842545 842545 1089 SDHC 210131_x_at 161284047 161284047 −554 TEX264 223964_x_at 51705248 51705248 −897 ENO3 204483_at 4854390 4854390 51 SETD3 229940_at 99947125 99947125 1752 TEX264 233350_s_at 51705248 51705248 −897 ATP5S 206993_at 50779047 50779047 −1123 ROCK2 202762_at 11484711 11484711 −1319 FOXN2 206708_at 48541849 48541849 −1059 WDR59 219586_at 75019017 75019017 −403 FAM161A 1564467_at 62081278 62081278 938 228565_at 233463514 233463514 1448 ZNF589 210062_s_at 48282590 48282590 −279 CAPN10 219333_s_at 241526133 241526133 1209 CTSB 200839_s_at 11725738 11725738 1705 DNTTIP1 224825_at 44420576 44420576 −685 RWDD4A 225574_at 184580378 184580378 898 ENSA 228852_at 150602053 150602053 −837 ADK 204120_s_at 75936444 75936444 925 SLC1A4 212811_x_at 65216535 65216535 1620 CD2BP2 202257_s_at 30366682 30366682 1079 CNIH4 223993_s_at 224544552 224544552 1458 RTEL1 206092_x_at 62289163 62289163 1455 208659_at 31698394 31698394 −257 ZNF697 227080_at 120190390 120190390 −1202 MBD4 214047_s_at 129158872 129158872 1171 C1orf58 239078_at 222885895 222885895 1590 MOSPD3 219070_s_at 100209725 100209725 −746 AASDH 235435_at 57253666 57253666 1168 C2orf47 219176_at 200820326 200820326 −1149 MMADHC 217883_at 150444330 150444330 −504 WDR33 223146_at 128568721 128568721 1416 LSM11 241599_at 157170755 157170755 −662 FN3KRP 218210_at 80674582 80674582 −760 NCBP1 209519_at 100395908 100395908 1543 UQCC 222470_s_at 33999944 33999944 −537 RBM33 238801_at 155437373 155437373 1591 C16orf88 213235_at 19726362 19726362 −780 SERBP1 228129_at 67896098 67896098 −1338 HIST1H3I 214509_at 27840093 27840093 743 NAGLU 204360_s_at 40687951 40687951 −298 ZNF668 219047_s_at 31085577 31085577 1801 BAG4 222909_s_at 38034312 38034312 −1369 C2orf79 226243_at 25016251 25016251 1083 ARL5B 226345_at 18948334 18948334 1567 ARG2 203945_at 68086579 68086579 −1290 BRD9 220155_s _at 892661 892661 646 PRPF4B 211090_s_at 4021560 4021560 −1778 TMEM79 223544_at 156252739 156252739 1110 ZBED3 228402_at 76383148 76383148 −909 MTIF3 223356_s_at 28024701 28024701 −1269 HNRNPA3 206809_s_at 178077477 178077477 −1180 PRPF4B 202126_at 4021560 4021560 −1778 RBM33 1554096_a_at 155437145 155437145 1819 BEAR 218056_at 14726672 14726672 −663 RPS15 200819_s_at 1438363 1438363 1364 RNASEN 218269_at 31532168 31532168 910 TMED9 205812_s_at 177019159 177019159 −863 DRAP1 203258_at 65686728 65686728 1284 HMGN4 209787_s_at 26538639 26538639 983 SDHC 215088_s_at 161284047 161284047 −554 MED20 206961_s_at 41888837 41888837 1004 ARL6IP1 211935_at 18812917 18812917 1596 FXC1 217981_s_at 6502690 6502690 976 ENSA 221486_at 150602053 150602053 −837 ASF1A 203428_s_at 119215384 119215384 1786 TSSC4 218612_s_at 2421718 2421718 1313 CISH 223377_x_at 50649203 50649203 1209 C6orf130 213322_at 41040330 41040330 1350 ENAH 222434_at 225840844 225840844 −1432 COG5 203629_s_at 107204485 107204485 −768 CISH 221223_x_at 50649203 50649203 1209 SFT2D3 226639_at 128458597 128458597 −163 DEPDC6 218858_at 120885900 120885900 −484 CDC20B 1564674_a_at 54469003 54469003 1625 LUC7L 220143_x_at 279462 279462 −443 ECHDC1 233124_s_at 127664745 127664745 −937 LARP4 212714_at 50794650 50794650 −669 SLC38A7 228951_at 58718674 58718674 −468 ZNF709 242028_at 12595643 12595643 −596 EHMT1 219339_s_at 140513454 140513454 −1226 C3orf19 1558094_s_at 14693271 14693271 859 FBXO34 218539_at 55738021 55738021 1504 SOCS4 226178_at 55493948 55493948 −1012 MBD4 209580_s_at 129158872 129158872 1171 ZNF828 226194_at 115079988 115079988 −943 FAM76B 232048_at 95522954 95522954 −1944 TMED2 204427_s_at 124069076 124069076 1130 RAB11FIP5 210879_s_at 73340146 73340146 1664 RTN3 224564_s_at 63448922 63448922 −566 RAB22A 218360_at 56884752 56884752 1334 RPL17 212270_x_at 47018906 47018906 1401 LUC7L 223546_x_at 279462 279462 443 E4F1 218524_at 2273567 2273567 1123 NFYA 215720_s_at 41040684 41040684 −1704 RPL27 200025_s_at 41150446 41150446 −1117 ECHDC1 223088_x_at 127664745 127664745 −937 POLR2H 209302_at 184079506 184079506 −1153 DTX3L 225415_at 122283085 122283085 −885 ZNF839 219086_at 102786096 102786096 −1405 RAD18 238748_at 9005186 9005186 −1043 ZNF251 226754_at 145980970 145980970 1083 MKLN1 242984_at 131012619 131012619 −1092 NEK3 213116_at 52733724 52733724 −347 ECHDC1 219974_x_at 127664745 127664745 −937 RTEL1 213829_x_at 62289163 62289163 1455 GOPC 227215_at 117923691 117923691 −918 SNX25 1555388_s_at 186125391 186125391 −1336 RPL17 212537_x_at 47018906 47018906 1401 ACOT13 204565_at 24667299 24667299 1079 NFX1 227651_at 33290510 33290510 1385 UBXN10 230092_at 20512578 20512578 −390 TMED2 204426_at 124069076 124069076 1130 PELI1 218319_at 64371588 64371588 −395 TMED9 208757_at 177019159 177019159 −863 AARSD1 238740_at 41132545 41132545 872 SNTB2 238925_at 69221032 69221032 1776 TIRAP 1552804_a_at 126152982 126152982 884 AAGAB 202852_s_at 67547074 67547074 1587 ZNHIT1 201541_s_at 100860949 100860949 −1051 RPL17 200038_s_at 47018906 47018906 1401 C2CD3 213199_at 73882064 73882064 −1356 DCP1A 218508_at 53381637 53381637 −702 SLC35F5 225872_at 114514400 114514400 −952 ZNF589 210061_at 48282590 48282590 −279 C4orf41 233558_s_at 184580420 184580420 −940 DUS4L 205762_s_at 107204403 107204403 850 ATP9B 214010_s_at 76829397 76829397 1305 KLHDC10 209256_s_at 129710350 129710350 −761 SDHC 216591_s_at 161284047 161284047 −554 DNAJC9 222499_at 75008620 75008620 202 WFDC3 232602_at 44420547 44420547 656 TUBG2 203894_at 40811266 40811266 −705 HNRNPH3 210588_x_at 70091832 70091832 −937 NEU3 216083_s_at 74699179 74699179 1847 NDUFB2 218201_at 140396471 140396471 1164 SUB1 224587_at 32585605 32585605 −384 ORC4L 203351_s_at 148778292 148778292 1406 CTTN 214074_s_at 70244650 70244650 −1139 GTF2E1 205930_at 120461579 120461579 1144 RANBP10 53987_at 67840555 67840555 1138 NDUFB6 203613_s_at 32573160 32573160 −531 U2AF2 218382_s_at 56165416 56165416 −663 PITPNA 201192_s_at 1466110 1466110 −660 GLE1 206921_at 131267010 131267010 −1114 HOOK2 218780_at 12886434 12886434 −591 PDS5B 207956_x_at 33160564 33160564 −993 HIST1H3F 208506_at 26250833 26250833 1259 MFAP1 203406_at 44117000 44117000 1126 FBXL18 220896_at 5553382 5553382 −959 FAU 200019_s_at 64889660 64889660 −817 CDC20B 1553655_at 54469003 54469003 1625 ANAPC16 224665_at 73975806 73975806 939 TRAF2 204413_at 139780970 139780970 −1023 MDN1 227797_x_at 90529442 90529442 −1030 MDN1 221311_x_at 90529442 90529442 −1030 KLHL36 219453_at 84682107 84682107 −776 EEPD1 1569640_s_at 36192758 36192758 −746 RANBP10 221809_at 67840555 67840555 1138 STUB1 227625_s_at 730276 730276 1185 SGTA 201396_s_at 2783315 2783315 −1418 PARN 203905_at 14724124 14724124 −436 AIDA 226801_s_at 222885866 222885866 −1619 C1orf151 224867_at 19923484 19923484 1271 CAMSAP1 220410_s_at 138799070 138799070 1398 GLE1 206920_s_at 131266979 131266979 −1083 FUBP1 214094_at 78444777 78444777 1860 STUB1 233049_x_at 730276 730276 1185 FUT10 239020_at 33330664 33330664 1935 ICMT 201611_s_at 6296000 6296000 1150 LRBA 212692_s_at 151936649 151936649 −1770 EHMT1 222873_s_at 140513454 140513454 −1226 FTL 213187_x_at 49468566 49468566 1083 GCA 203765_at 163200598 163200598 −467 VHL 1559227_s_at 10182692 10182692 0 C20orf11 218448_at 61569471 61569471 1046 GLE1 225371_at 131266979 131266979 −1083 ZMYND10 216663_s_at 50384283 50384283 619 UTP23 227402_s_at 117778742 117778742 −638 ZNF800 227101_at 127032745 127032745 1842 ANAPC16 224664_at 73975806 73975806 939 CCDC101 221822_at 28565247 28565247 −355 LSM1 203534_at 38034026 38034026 1083 ZXDC 218639_s_at 126194762 126194762 −909 CISH 223961_s_at 50649203 50649203 1209 MAP2K7 209952_s_at 7968776 7968776 −1199 RPS13 200018_at 17099220 17099220 −1085 MSH3 205887_x_at 79950467 79950467 1119 NFX1 202584_at 33290509 33290509 1386 TM7SF3 217974_at 27167339 27167339 −778 SSNA1 210378_s_at 140083099 140083099 1189 JAG1 209097_s_at 10654608 10654608 −1306 RFESD 236305_at 94982458 94982458 1311 RPRD2 235415_at 150337126 150337126 −1601 GSTK1 217751_at 142960522 142960522 1050 SNORD118 235490_at 8079714 8079714 −807 TGM2 211003_x_at 36793774 36793774 439 PDDC1 227968_at 777484 777484 −940 E2F1 2028_s_at 32274210 32274210 −665 FKBP15 212663_at 115983598 115983598 −1373 ZNF839 221709_s_at 102786096 102786096 −1405 ACOX3 204242_s_at 8442450 8442450 −1197 LYPLA2 215568_x_at 24117460 24117460 −518 ZC3H4 213390_at 47617009 47617009 −648 TRIM41 226445_s_at 180650290 180650290 −1526 NDUFB2 218200_s_at 140396471 140396471 1164 CYB561D2 209665_at 50388126 50388126 752 HNRNPH3 207127_s_at 70091832 70091832 −937 MBLAC1 1554170_a_at 99724317 99724317 −876 C11orf68 221534_at 65686531 65686531 −1481 STUB1 217934_x_at 730276 730276 1185 GTF2B 208066_s_at 89357301 89357301 −787 36019_at 31939608 31939608 −414 UBR3 241244_at 170684018 170684018 −1624 IQCK 215130_s_at 19727778 19727778 0 RANBP10 1558773_s_at 67840555 67840555 1138 CAPN1 200752_s_at 64949343 64949343 965 EFR3A 212149_at 132916335 132916335 −556 TATDN2 203648_at 10289707 10289707 −121 ADIPOR1 217748_at 202927517 202927517 1164 SLC48A1 218416_s_at 48166991 48166991 −497 C2CD3 231708_at 73882064 73882064 −1356 POLR2L 202586_at 842545 842545 1089 SLC38A7 218727_at 58718674 58718674 −468 ZNF697 1553702_at 120190390 120190390 −1202 USP4 211800_s_at 49377466 49377466 −780 208273_at 247171210 247171210 827 NDUFB2 240391_at 140396471 140396471 1164 RRAGA 201628_s_at 19049372 19049372 −739 FAM161A 239090_at 62081278 62081278 938 ANGEL2 217630_at 213189168 213189168 −548 RAD18 238670_at 9005186 9005186 −1043 FBXO31 224162_s_at 87417394 87417394 1495 TATDN2 1565580_s_at 10289707 10289707 −121 DNAJC9 229701_at 75008620 75008620 202 RNF181 223064_at 85822857 85822857 −897 PXMP2 1553837_at 133287436 133287436 888 COPE 201264_at 19030199 19030199 860 RPL41 201492_s_at 56510572 56510572 −1285 WHSC2 244260_at 2011837 2011837 −276 TMED2 200087_s_at 124069076 124069076 1130 RPS28 208904_s_at 8386384 8386384 −1135 TRPC4AP 212059_s_at 33680674 33680674 −482 C1orf56 230468_s_at 151020216 151020216 −485 CCDC101 48117_at 28565247 28565247 −355 FKBP15 31826_at 115983598 115983598 −1373 C19orf55 242640_at 36249117 36249117 800 SLC39A1 217778_at 153936048 153936048 −1038 C3orf1 223004_s_at 119217379 119217379 −789 ZNF410 202010_s_at 74353574 74353574 1619 RANGRF 223554_s_at 8191989 8191989 −832 RPTOR 225715_at 78518625 78518625 −763 HARBI1 241498_at 46638777 46638777 689 FAM192A 222460_a_at 57219976 57219976 1155 RABEPK 1558021_at 127962824 127962824 −917 MORF4 221381_s_at 79165211 79165211 −973 ARMC2 223866_at 109169625 109169625 −528 UBAP1 46270_at 34179011 34179011 1216 KIAA1430 1554550_at 186125182 186125182 1127 SNORD73A 201257_x_at 152020725 152020725 1741 EIF4G2 200004_at 10830017 10830017 −1755 SNORD73A 200099_s_at 152020725 152020725 1741 SNORD73A 212391_x_at 152020725 152020725 1741

TABLE 15 Genes with higher gene expression variability in cancer compared to normal. gene dist2block dist2PMD dist2DMR dist2CGI p-value Cancer % On Normal % On chr strand txStart txEnd affyid blockStart blockEnd DSC3 3043 0 1724347 0 9.29E−08 12 0 chr18 −1 28570052 28622781 206032_at 28625824 28638204 CXCL5 177140 433359 53823 166 9.29E−08 21 0 chr4 −1 74861359 74864496 214974_x_at 74642141 74687356 PAH 0 0 37070 127 9.29E−08 8 0 chr12 −1 103232104 103311381 205719_s_at 103311276 103339573 CXCL5 177140 433359 53823 166 1.39E−07 21 0 chr4 −1 74861359 74864496 215101_s_at 74642141 74687356 INHBA 0 660770 183342 2473 3.17E−07 67 0 chr7 −1 41724712 41742706 227140_at 40180732 41744986 MMP10 0 1366568 311747 310916 4.18E−07 67 0 chr11 −1 102641245 102651359 205680_at 102461598 102927599 LPL 7052 0 0 560 8.05E−07 50 0 chr8 1 19796284 19824769 203548_s_at 19803336 20054515 SLCO1B3 0 4904 439417 257633 1.01E−06 71 0 chr12 1 20963638 21069658 206354_at 20541064 21590451 SRPX2 67966 0 1480794 7420 1.07E−06 67 0 chrX 1 99899215 99926296 205499_at 99676689 99831249 STC1 0 138264 126756 127558 1.09E−06 29 0 chr8 −1 23699428 23712320 204597_x_at 23587917 24765322 CA2 4312 0 1278765 0 1.09E−06 100 100 chr8 1 86376131 86393721 209301_at 86360205 86371819 CXCL11 0 203627 29629 45097 1.73E−06 75 0 chr4 −1 76954835 76957350 211122_s_at 76956471 76975325 STC1 0 138264 126756 127558 1.78E−06 12 0 chr8 −1 23699428 23712320 204595_s_at 23587917 24765322 IL13RA2 0 0 214202 170371 1.89E−06 46 0 chrX −1 114238538 114253536 206172_at 113834443 114461778 CLDN1 61858 407043 1166 0 3.46E−06 46 0 chr3 −1 190023490 190040264 218182_s_at 189951990 189978406 SLC35D3 29910 34906 930 0 3.78E−06 33 0 chr6 1 137243402 137246777 231341_at 137273312 137298915 EPHX4 197 441874 0 0 3.78E−06 42 0 chr1 1 92495539 92529093 239579_at 92358039 92495342 ACSL6 464 0 13 0 4.06E−06 33 0 chr5 −1 131285666 131347355 229725_at 131347819 131524774 CCL26 0 420490 148093 32496 4.37E−06 17 0 chr7 −1 75398851 75401575 223710_at 75369111 75503808 CST1 0 0 327852 112934 4.39E−06 42 0 chr20 −1 23728190 23731574 206224_at 23641665 24442368 MAGEA6 0 0 60268 0 5.60E−06 4 0 chrX 1 151867214 151870825 209942_x_at 151863274 151869775 GIF 73110 0 35703 34594 5.91E−06 75 0 chr11 −1 59596748 59612974 207033_at 59686084 59872871 ZIC2 23214 0 3338 0 8.36E−06 4 0 chr13 1 100634026 100639018 223642_at 100657240 100718965 TCN1 52043 0 56770 31539 8.36E−06 100 0 chr11 −1 59620284 59634041 205513_at 59686084 59872871 C8orf84 385 0 203092 0 8.97E−06 67 0 chr8 −1 73978132 74005507 235209_at 74005892 74199003 MMP7 0 1116667 61846 77695 8.97E−06 100 0 chr11 −1 102391268 102401458 204259_at 102352665 102432092 REG4 27196 95725 162475 41607 8.97E−06 50 0 chr1 −1 120343793 120354203 238984_at 120309254 120327007 C8orf84 385 0 203092 0 1.12E−05 79 0 chr8 −1 73978132 74005507 235210_s_at 74005892 74199003 KRT6A 0 0 107645 107801 1.12E−05 8 0 chr12 −1 52880958 52886972 209125_at 52702607 53107910 CHI3L1 0 27501 45438 58380 1.12E−05 79 0 chr1 −1 203148059 203155877 209395_at 203097543 203236398 SIM2 13424 0 955 0 1.34E−05 8 0 chr21 1 38071434 38122218 241726_at 37854364 38058010 CLDN2 0 0 352095 78873 1.34E−05 96 0 chrX 1 106163634 106174091 223509_at 106114542 106178629 LRP8 6542 23727 236781 189 1.34E−05 38 0 chr1 −1 53711217 53793686 205282_at 53800228 54201098 KRT6B 0 0 94307 84810 1.37E−05 50 0 chr12 −1 52840437 52845910 213680_at 52702607 53107910 TAC1 11501 0 0 0 1.37E−05 21 0 chr7 1 97361220 97369784 206552_s_at 96804192 97349719 ULBP2 27393 0 6084 0 1.38E−05 12 0 chr6 1 150263136 150270371 238542_at 150290529 150301470 ZG16 0 1422910 6544 6772 1.42E−05 96 100 chr16 1 29789590 29792969 214142_at 29776286 29790986 COL11A1 0 0 0 494441 1.42E−05 4 0 chr1 −1 103342023 103574047 37892_at 101706840 103791505 KRT23 0 117197 18451 73570 1.50E−05 33 0 chr17 −1 39078948 39093672 218963_s_at 39079223 39102520 CADPS 0 0 102346 103213 1.54E−05 79 0 chr3 −1 62384023 62467530 1568603_at 62439298 62528066 WISP3 0 851967 33840 33132 1.55E−05 17 0 chr6 1 112375275 112390889 210861_s_at 112194877 112392175 GPR109B 0 1056158 45936 49105 1.68E−05 8 0 chr12 −1 123185840 123187890 205220_at 123128681 123233349 PCCA 22372 89337 11076 0 1.69E−05 100 100 chr13 1 100741337 101182686 203860_at 100657240 100718965 MMP3 0 1429529 374708 247955 1.73E−05 96 0 chr11 −1 102706532 102714320 205828_at 102461598 102927599 CEL 13070 47185 19830 9222 1.86E−05 4 0 chr9 1 135937365 135947248 205910_s_at 135950435 135964747 IL1A 0 111363 351669 19592 2.12E−05 17 0 chr2 −1 113531492 113542167 210118_s_at 113535635 113544577 CHI3L1 0 27501 45438 58380 2.50E−05 71 0 chr1 −1 203148059 203155877 209396_s_at 203097543 203236398 TMPRSS3 0 0 0 89883 2.64E−05 8 0 chr21 −1 43801985 43816200 223949_at 43805856 43823604 ACSL6 464 0 13 0 2.64E−05 46 0 chr5 −1 131285666 131347355 211207_s_at 131347819 131524774 SERPINE1 1942 32911 30688 27163 2.85E−05 12 0 chr7 1 100770370 100782547 202628_s_at 100701852 100768428 SLC28A3 0 0 328881 199897 2.92E−05 79 0 chr9 −1 86890372 86955598 232277_at 86933053 87278151 TNIP3 0 25056 215296 91791 3.13E−05 4 0 chr4 −1 122052563 122085495 220655_at 121997815 122289891 MAGEA6 0 0 60268 0 3.27E−05 4 0 chrX 1 151867214 151870825 214612_x_at 151863274 151869775 TACSTD2 4441 0 421 0 3.43E−05 96 0 chr1 −1 59041099 59043166 202286_s_at 59013255 59038725 DEFB4A 9169 9560 730487 60370 3.63E−05 4 0 chr8 1 7752151 7754233 207356_at 7731334 7742982 PHLDA1 48055 741822 731051 0 3.63E−05 75 0 chr12 −1 76419227 76425556 217999_s_at 76344741 76377501 PRDM13 16559 0 0 81 3.73E−05 4 0 chr6 1 100054606 100062635 221168_at 100071165 100441380 PDPN 97 0 0 117 3.90E−05 8 0 chr1 1 13909960 13944452 221898_at 13844945 13909863 KRT80 45942 117950 40964 39420 3.94E−05 54 0 chr12 −1 52562780 52585784 231849_at 52481071 52539842 PTPN13 6744 174491 296250 0 3.94E−05 54 0 chr4 1 87515468 87736310 204201_s_at 87484267 87508724 ACSL6 464 0 13 0 3.96E−05 12 0 chr5 −1 131285666 131347355 213683_at 131347819 131524774 MSX2 8523 0 77 0 4.04E−05 83 0 chr5 1 174151536 174157902 210319_x_at 174137456 174143013 HS6ST2 9861 0 1214351 0 4.37E−05 33 0 chrX −1 131760038 132091358 230030_at 132101219 132274423 MSX2 8523 0 77 0 4.37E−05 88 0 chr5 1 174151536 174157902 205555_s_at 174137456 174143013 DSC3 3043 0 1724347 0 4.80E−05 12 0 chr18 −1 28570052 28622781 206033_s_at 28625824 28638204 ARNTL2 47335 1197254 1004 0 5.00E−05 79 0 chr12 1 27485988 27573466 220658_s_at 27397668 27438653 CLDN1 61858 407043 1166 0 5.14E−05 92 0 chr3 −1 190023490 190040264 222549_at 189951990 189978406 CA1 22155 0 1164764 88636 5.42E−05 67 100 chr8 −1 86240458 86262130 205950_s_at 86284285 86332544 BMP7 5454 0 0 0 5.47E−05 17 0 chr20 −1 55743804 55841684 209591_s_at 55847138 55925397 SERPINE1 1942 32911 30688 27163 5.80E−05 8 0 chr7 1 100770370 100782547 202627_s_at 100701852 100768428 REG1B 0 0 93943 94526 5.80E−05 46 8 chr2 −1 79312157 79315119 205886_at 79220617 79739679 CEACAM7 11681 0 120452 156380 6.15E−05 100 100 chr19 −1 42177235 42192296 206199_at 42168674 42180615 WDR72 0 0 2906 3070 6.20E−05 25 0 chr15 −1 53805938 54055075 236741_at 54052067 55473630 HOXA10 25501 0 518 129 6.26E−05 100 100 chr7 −1 27210852 27219880 213150_at 27245381 27250842 SERPIND1 1422 138166 102460 69373 6.50E−05 4 0 chr22 1 21128167 21142008 205576_at 21129589 21137392 LRRC34 15 73145 8885 16 6.67E−05 12 0 chr3 −1 169511216 169530452 236918_s_at 169530467 169549519 CA9 40997 203852 147 1796 7.21E−05 29 0 chr9 1 35673853 35681156 205199_at 35621412 35632856 RAI2 6717 0 1134625 0 7.51E−05 38 54 chrX −1 17818171 17879356 219440_at 17772790 17872639 PCDHB9 56150 0 22029 1472 7.60E−05 33 0 chr5 1 140571952 140575213 223854_at 140493790 140515802 VSIG1 0 0 108613 46177 8.05E−05 8 0 chrX 1 107288244 107322327 243764_at 107183860 107324359 PTGS2 276 433823 1362224 0 8.13E−05 17 0 chr1 −1 186640923 186649555 1554997_s_at 186400111 186649279 TCEA3 35942 236181 57047 0 8.65E−05 100 100 chr1 −1 23707554 23751233 226388_at 23787175 23806389 C8orf84 385 0 203092 0 9.17E−05 33 0 chr8 −1 73976780 74005507 230661_at 74005892 74199003 SLC7A11 13988 1242952 1036798 318232 9.84E−05 92 17 chr4 −1 139085251 139163503 209921_at 139177491 139929775 FAP 0 91710 99867 100531 0.000103138 4 0 chr2 −1 163027200 163100045 209955_s_at 163054893 163117608 CDH3 10717 0 109640 0 0.000109956 88 0 chr16 1 68678739 68732971 203256_at 68600291 68668022 FABP1 0 0 73419 42057 0.000110684 100 100 chr2 −1 88422510 88427635 205892_s_at 88427215 88441743 PADI2 13112 18516 29773 0 0.000111884 96 100 chr1 −1 17393256 17445930 209791_at 17459042 17465128 DUSP4 13858 0 178908 0 0.000117074 33 0 chr8 −1 29190581 29208185 226034_at 29139381 29194327 C2CD4A 2804 13533 2160 652 0.000117391 96 0 chr15 1 62359176 62363109 241031_at 62361980 62380410 S100A12 0 0 113621 160300 0.000117807 0 0 chr1 −1 153346184 153348125 205863_at 153243308 153489968 DSG3 54535 0 1319370 49795 0.00011886 8 0 chr18 1 29027758 29058665 235075_at 29082293 29096608 ART3 0 228624 4632 20100 0.000121332 71 0 chr4 1 76932353 77033955 210147_at 76919327 76934310 ADAM12 5580 42987 0 0 0.000122955 4 0 chr10 −1 127700950 128077024 226777_at 128082604 128586018 CEL 13070 47185 19830 9222 0.000126064 4 0 chr9 1 135937365 135947248 1553970_s_at 135950435 135964747 SLC4A4 5471 428134 2044 0 0.000130954 96 100 chr4 1 72053003 72435434 203908_at 72058474 73433711 PTGES 0 494854 20546 14772 0.00013104 0 0 chr9 −1 132500610 132515326 210367_s_at 132512031 132561852 SLAIN1 232 0 217279 0 0.00014771 8 0 chr13 1 78272023 78338259 225619_at 77904087 78271791 TNFRSF11B 275 186437 254731 7 0.00014771 25 0 chr8 −1 119935797 119964383 204932_at 119964658 120167597 MYO1A 25283 60167 88409 28374 0.000157753 100 100 chr12 −1 57422301 57443901 211916_s_at 57405720 57418618 C15orf48 32564 30098 241689 0 0.000170778 100 100 chr15 1 45722807 45725647 223484_at 45684488 45690243 NME5 0 96998 0 39557 0.00017316 29 0 chr5 −1 137450866 137475104 206197_at 137375472 137501136 HS6ST2 9861 0 1214351 0 0.000174438 4 0 chrX −1 131760038 132091358 1552766_at 132101219 132274423 RNF183 78021 151296 3884 23246 0.000178243 58 0 chr9 −1 116059480 116061476 235153_at 116139497 116148523 ELF5 0 10079 91338 72488 0.000179381 4 0 chr11 −1 34500342 34533346 220625_s_at 34494011 34594197 ONECUT2 14893 0 3622 208 0.000185671 4 0 chr18 1 55102917 55158530 239911_at 55021604 55088024 ALKBH3 45238 81068 720 0 0.000190181 29 4 chr11 1 43902357 43941823 226127_at 43947595 43956807 SLC7A11 13988 1242952 1036798 318232 0.000192417 25 0 chr4 −1 139085251 139163503 207528_s_at 139177491 139929775 KIAA1549 4077 166603 19826 295 0.000212477 0 0 chr7 −1 138516126 138666064 223575_at 138670141 138700109 FAM40B 56013 281509 56881 0 0.000213786 8 0 chr7 1 129074274 129128240 231880_at 128993853 129018261 SLC26A2 32757 179508 228976 0 0.000227716 100 100 chr5 1 149340300 149366968 205097_at 149286630 149307543 IL24 0 17411 154100 11905 0.000229307 0 0 chr1 1 207070789 207077210 206569_at 206911264 207078912 KLK6 0 0 47520 32986 0.000242481 38 0 chr19 −1 51461888 51472929 204733_at 51416341 51518249 CYP4X1 7364 0 202593 0 0.00024585 92 0 chr1 1 47489240 47516423 227702_at 47190239 47481876 CCDC113 6027 1363 212841 0 0.000247123 75 0 chr16 1 58283863 58317740 222890_at 58234237 58277836 TRIB3 4872 119260 19871 229 0.000248853 17 0 chr20 1 361261 378203 1555788_a_at 345685 356389 CXCL6 14858 271077 107500 207 0.000261126 25 0 chr4 1 74702214 74704477 206336_at 74642141 74687356 KRT17 0 4354 109288 23912 0.000261126 8 0 chr17 −1 39775689 39780829 205157_s_at 39711383 39800097 CKMT2 27560 654859 19763 68217 0.000283189 4 0 chr5 1 80529104 80562216 205295_at 80495827 80501544 STC2 3650 59111 12552 0 0.000283189 4 0 chr5 −1 172741716 172756506 203438_at 172760156 173021332 NMU 6001 0 157023 0 0.000289919 100 29 chr4 −1 56461398 56502465 206023_at 56508466 56603043 CPS1 0 0 784146 79725 0.00029186 21 0 chr2 1 211421262 211543831 217564_s_at 211343341 213393136 PSAT1 4606 81878 309115 0 0.000301096 83 0 chr9 1 80912059 80945009 220892_s_at 80894673 80907453 MAGEA11 0 27700 759730 56214 0.000301842 4 0 chrX 1 148769894 148797942 210503_at 148749972 148848717 GAL 5837 718558 415 0 0.000302226 33 0 chr11 1 68451983 68458643 214240_at 68381628 68446146 RTEL1 23159 171199 0 293 0.000302707 33 0 chr20 1 62290756 62330051 206467_x_at 62313915 62327968 IL1B 16253 59050 319384 71905 0.000303787 38 0 chr2 −1 113587328 113594480 39402_at 113610733 113629323 SNTB1 9028 883489 685812 0 0.000316413 42 0 chr8 −1 121547985 121824309 214708_at 121833337 122288541 PHGDH 0 0 62782 335 0.000327764 33 0 chr1 1 120254510 120286838 201397_at 120200649 120254790 ITLN1 0 0 96438 83006 0.000359862 100 100 chr1 −1 160846329 160854960 223597_at 160549158 160942166 DUSP27 0 0 25138 27294 0.000359862 62 0 chr1 1 167063282 167098366 232252_at 167045377 167065026 ALPK3 46220 339086 548054 282 0.000361358 21 0 chr15 1 85359911 85416713 228342_s_at 85406131 85454098 CES2 18044 214137 40796 0 0.000361478 100 100 chr16 1 66968363 66978999 209667_at 66940239 66950319 VAV2 7763 337252 3505 0 0.000364999 0 71 chr9 −1 136627016 136857432 226063_at 136865195 136884947 ADAMDEC1 0 0 528257 529037 0.000366542 100 100 chr8 1 24241872 24263526 206134_at 23587917 24765322 ODAM 0 0 992834 491642 0.000373326 79 0 chr4 1 71062213 71070293 220133_at 70727714 71551169 TTC26 134 319063 96385 0 0.000376398 0 0 chr7 1 138818524 138876732 235949_at 138818658 138824296 SLC6A6 578 110921 590 0 0.000386778 12 0 chr3 1 14444076 14530857 205921_s_at 14444654 14452211 TMEM17 6750 56979 198513 0 0.000395806 8 0 chr2 −1 62727356 62733476 1557137_at 62740226 62870904 DSC3 3043 0 1724347 0 0.000415129 12 0 chr18 −1 28570052 28622781 244107_at 28625824 28638204 PKIB 321 0 209064 0 0.000427117 100 100 chr6 1 122931377 123047037 223551_at 122804831 122931056 CXCR2 0 0 198359 90927 0.00043038 12 0 chr2 1 218990727 219001976 207008_at 218875402 219075651 SERPINA3 0 0 14178 155979 0.000448005 50 0 chr14 1 95078634 95090397 202376_at 95071921 95226467 FAM176A 13377 141546 0 0 0.000455315 0 0 chr2 −1 75719444 75788039 227828_s_at 75801416 75869723 COL11A1 0 0 0 494441 0.000455576 4 0 chr1 −1 103342023 103574047 204320_at 101706840 103791505 AP1S3 88506 450562 108395 0 0.000455576 92 12 chr2 −1 224616403 224702319 1555731_a_at 224584621 224613813 GRHL1 4565 1540723 61525 0 0.000466402 46 0 chr2 1 10091827 10142405 222830_at 10077338 10087262 SLC26A2 32757 179508 228976 0 0.000470422 100 100 chr5 1 149340300 149366968 224959_at 149286630 149307543 KCNJ15 0 99468 339397 339395 0.000492912 4 0 chr21 1 39628663 39673743 210119_at 39300209 39888752 DDIT4L 9870 19353 0 127 0.000495686 0 0 chr4 −1 101107027 101111625 228057_at 100876732 101101755 4417 2070 148395 17655 0.0004971 4 0 chr6 −1 30899130 30899952 244056_at 30904369 30923128 HS6ST2 9861 0 1214351 0 0.000506632 50 4 chrX −1 131760038 132091358 1552767_a_at 132101219 132274423 SERPINB4 0 0 292763 221174 0.000507296 8 0 chr18 −1 61304493 61311532 209720_s_at 61174562 61603221 PROK2 7372 0 0 0 0.00050836 0 0 chr3 −1 71820807 71834357 232629_at 71841729 72200853 SLCO3A1 4664 7928 61741 0 0.000514943 4 0 chr15 1 92396925 92709133 219229_at 92090952 92392261 DKK1 3687 335939 1893734 0 0.000525644 12 0 chr10 1 54074056 54077417 204602_at 54077743 54709456 SERPINB7 0 23623 161651 160757 0.000527835 4 0 chr18 1 61442644 61472604 206421_s_at 61174562 61603221 ASB9 0 0 519278 65100 0.000547606 50 0 chrX −1 15262109 15288270 205673_s_at 15279573 15314091 CHST4 0 0 84153 63775 0.00055017 12 0 chr16 1 71560036 71572488 220446_s_at 71508877 71649407 TESC 6115 0 43582 0 0.000554983 33 0 chr12 −1 117476729 117537274 218872_at 117515108 117531159 IL8 35918 175086 203491 96198 0.000563037 88 0 chr4 1 74606223 74609433 211506_s_at 74642141 74687356 TRIB3 4872 119260 19871 229 0.00056632 58 0 chr20 1 361261 378203 218145_at 345685 356389 SLC16A4 21634 24830 17520 16245 0.000571565 50 0 chr1 −1 110905482 110933648 205234_at 110955282 111098047 PAX9 13797 0 31 5 0.000589145 0 0 chr14 1 37126782 37147007 231145_at 37059570 37112985 GABRP 0 0 279091 38924 0.000596619 46 0 chr5 1 170210723 170241051 205044_at 170176247 170287040 HES6 3526 296497 8396 0 0.000600568 96 46 chr2 −1 239146908 239148765 226446_at 239114888 239145239 FCGR3B 11381 12381 9312 18618 0.00061377 29 0 chr1 −1 161592986 161600996 204007_at 161612377 161624111 IL6 0 302027 174951 60081 0.000615947 4 0 chr7 1 22765503 22771621 205207_at 22589544 22845416 GAD1 7116 0 1433 0 0.000615947 4 0 chr2 1 171673072 171717661 205278_at 171642386 171665956 FAM92A1 1711 491948 138 0 0.000623382 75 0 chr8 1 94712773 94740669 235391_at 93986519 94711062 NRCAM 0 115683 152289 153023 0.000634468 17 0 chr7 −1 107788094 107797082 204105_s_at 107660496 108089223 DHRS2 3771 0 52475 52617 0.000637004 4 0 chr14 1 24099378 24113734 214079_at 24103149 24412077 KLK12 0 0 17019 2672 0.00065012 50 0 chr19 −1 51532348 51538148 220782_x_at 51523889 51568096 S100A2 65 64964 1056 29500 0.000669388 88 0 chr1 −1 153533584 153538341 204268_at 153538406 153589115 KLK10 458 0 2302 627 0.000689459 83 0 chr19 −1 51516001 51523431 209792_s_at 51523889 51568096 SOX1 13118 0 0 0 0.000691062 4 0 chr13 1 112721913 112726020 237472_at 112735031 112751564 BNIP3 9283 14576 0 0 0.000719793 54 62 chr10 −1 133781578 133795435 201849_at 133804718 133843600 HEPACAM2 0 0 347647 182820 0.000736786 100 100 chr7 −1 92817899 92855837 242601_at 92468948 92863507 DUSP4 13858 0 178908 0 0.000740191 46 0 chr8 −1 29190581 29208185 204014_at 29139381 29194327 C12orf48 6330 151915 822 0 0.000740191 83 0 chr12 1 102513956 102591298 220060_s_at 102520286 102528156 FZD3 9953 0 130703 0 0.00074544 4 0 chr8 1 28351773 28431788 227499_at 28335606 28341820 PLCE1 40899 160558 34595 36367 0.000769807 100 100 chr10 1 95790569 96088146 205112_at 95693652 95749670 ANXA9 63673 728884 64891 6542 0.000778227 4 0 chr1 1 150954493 150968110 211712_s_at 150852840 150890820 KCNMA1 5882 451642 229 0 0.000780843 100 100 chr10 −1 78644639 79398353 221584_s_at 77832723 79392471 CLCA1 0 0 311181 71967 0.000793251 100 100 chr1 1 86934051 86965942 210107_at 86862111 86977585 SLC26A3 15586 0 56970 58630 0.000795509 100 100 chr7 −1 107405917 107443652 206143_at 107459238 107531437 AP1S3 88506 450562 108395 0 0.000828049 96 0 chr2 −1 224616403 224702319 1555733_s_at 224584621 224613813 SCARA5 0 0 99938 70430 0.000859851 75 100 chr8 −1 27727399 27850198 229839_at 27695516 27942212 MALL 0 71431 2237 555 0.000869551 100 100 chr2 −1 110841447 110874143 209373_at 110873609 110962342 TNS4 0 58626 537 57542 0.000879134 67 0 chr17 −1 38632080 38657849 230398_at 38645632 38669338 PROM2 0 3927 0 66652 0.000901221 100 100 chr2 1 95940201 95957054 1552797_s_at 95939815 96011110 DUSP4 13858 0 178908 0 0.000904271 54 0 chr8 −1 29190581 29208185 204015_s_at 29139381 29194327 SLC6A14 0 0 1098999 482392 0.000936009 79 17 chrX 1 115567790 115592625 219795_at 115555306 115682087 IL1B 16253 59050 319384 71905 0.000962689 42 0 chr2 −1 113587328 113594480 205067_at 113610733 113629323 FAIM2 11804 46014 0 0 0.000964227 58 0 chr12 −1 50260680 50297720 203619_s_at 50280106 50285916 SNTB1 9028 883489 685812 0 0.000983371 38 0 chr8 −1 121547985 121824309 208608_s_at 121833337 122288541 IL11 1283 183625 2042 891 0.000995344 0 0 chr19 −1 55875757 55881814 206924_at 55866329 55880531 IL17A 0 0 476841 97965 0.001006616 0 0 chr6 1 52051185 52055436 216876_s_at 50824075 52126759 C13orf18 164 10379 1112 0 0.001013305 96 100 chr13 −1 46917099 46961621 219471_at 46961785 46974863 CES2 18044 214137 40796 0 0.001013305 71 100 chr16 1 66968363 66978999 213509_x_at 66940239 66950319 TMPRSS3 0 0 301 90638 0.001022735 21 0 chr21 −1 43791999 43816955 220177_s_at 43805856 43823604 ESM1 0 17247 101321 101319 0.001039369 0 0 chr5 −1 54273692 54281491 208394_x_at 54182326 54468722 FREM2 8369 0 0 0 0.001043428 38 0 chr13 1 39261266 39460074 230964_at 39269635 39581012 KIAA1199 70807 341262 810 0 0.001052308 79 0 chr15 1 81071684 81244117 1554685_a_at 80992262 81000877 IGFL2 2793 0 124992 69055 0.001072308 17 0 chr19 1 46651500 46664559 231148_at 46581016 46648707 SLC26A2 32757 179508 228976 0 0.001084707 88 100 chr5 1 149340300 149366968 224963_at 149286630 149307543 C8orf84 385 0 203092 0 0.00109793 0 0 chr8 −1 73978132 74005507 214725_at 74005892 74199003 TSPAN1 6480 236655 22728 7826 0.001100033 100 100 chr1 1 46640759 46651630 209114_at 46647239 46652840 STC1 0 138264 126756 127558 0.001118866 8 0 chr8 −1 23699428 23712320 204596_s_at 23587917 24765322 GPR37 5278 177084 588 0 0.001135355 8 0 chr7 −1 124386051 124405681 209631_s_at 124410959 124470571 5912 0 940 22 0.001162416 88 100 chr16 1 23765948 23770272 206149_at 23727829 23760036 TMEM182 104499 29798 113058 0 0.001185773 33 0 chr2 1 103353367 103433875 238867_at 103457866 105456231 FRMD5 470 475280 93258 0 0.00118591 25 0 chr15 −1 44162962 44487429 230831_at 44487899 44575216 TTC9 8629 0 386549 0 0.001191826 8 0 chr14 1 71108504 71142077 213172_at 71072550 71099875 DSG3 54535 0 1319370 49795 0.00119268 8 0 chr18 1 29027758 29058665 205595_at 29082293 29096608 SEMA6A 5595 0 1644 0 0.001199877 92 100 chr5 −1 115779312 115910630 223449_at 115916225 118236347 AZGP1 0 21715 0 21427 0.001206646 92 25 chr7 −1 99564353 99573780 209309_at 99559725 99587874 SERPINA7 0 0 214154 214274 0.001218309 4 0 chrX −1 105277197 105281385 206386_at 105078443 105854952 GRIN2D 68402 339943 2509 932 0.001224705 62 0 chr19 1 48898132 48948187 229883_at 48966534 48971598 KIAA0802 0 107368 108401 9811 0.00122728 17 0 chr18 1 8717369 8832776 213358_at 8716599 8784601 UNC93A 0 0 374649 59720 0.001232525 0 0 chr6 1 167704803 167729507 214382_at 167702535 167760131 TNFRSF10C 11022 216376 0 0 0.001277837 8 0 chr8 1 22960432 22974950 206222_at 22942117 22949410 AMIGO2 10567 350000 247537 0 0.001281293 75 96 chr12 −1 47469490 47473734 222108_at 47233188 47463167 HOXA10 40252 0 9331 0 0.001281293 100 100 chr7 −1 27202057 27205129 214651_s_at 27245381 27250842 PCDHA6 9260 0 41430 76 0.001281293 12 0 chr5 1 140207650 140391929 210674_s_at 140189536 140198390 CYP1B1 7396 296826 0 0 0.001302935 8 0 chr2 −1 38294652 38303323 202435_s_at 38253683 38295927 PLEKHB1 0 314870 46796 14578 0.001304027 88 33 chr11 1 73357223 73373862 209504_s_at 73309661 73366647 LRP8 6542 23727 236781 189 0.001312395 21 0 chr1 −1 53711217 53793686 208433_s_at 53800228 54201098 SEMG1 0 0 108281 86312 0.001314082 4 0 chr20 1 43835638 43838413 206442_at 43734130 43921921 SPRR1A 0 0 275572 224368 0.001314082 8 0 chr1 1 152957707 152957976 213796_at 152590080 153227464 DDC 51941 0 2920 92797 0.001326413 100 100 chr7 −1 50526134 50628751 205311_at 50680692 50851568 BRCA2 96 447610 224177 0 0.001339698 25 0 chr13 1 32889611 32973347 208368_s_at 32605926 32889515 LRRC34 15 73145 8885 16 0.001339698 4 0 chr3 −1 169511216 169530452 236917_at 169530467 169549519 PTP4A3 6191 28812 95970 3655 0.001354276 8 0 chr8 1 142432007 142441620 209695_at 142438198 142528142 KRT20 0 65004 0 21377 0.001374569 100 100 chr17 −1 39030852 39041479 213953_at 39041424 39053830 IMPA2 5934 118574 56859 0 0.001377702 100 100 chr18 1 11981427 12030876 203126_at 11953602 11975493 FCGBP 59730 0 10001 9921 0.001386452 100 100 chr19 −1 40353964 40440533 203240_at 40339674 40380803 MMP19 0 123001 23793 12422 0.001426821 4 0 chr12 −1 56229244 56236735 204575_s_at 56228700 56291334 FANCI 6706 91817 116018 0 0.001438878 92 17 chr15 1 89787180 89860492 213008_at 89745309 89780474 ALDH1A2 4835 0 0 0 0.001451445 8 0 chr15 −1 58245622 58358616 207016_s_at 58363451 58617872 GOLM1 15636 65708 576489 0 0.001481535 100 100 chr9 −1 88641061 88714473 217771_at 88730109 88871030 LIMCH1 871 0 102792 0 0.00148522 83 8 chr4 1 41362802 41701029 212325_at 41363673 41742043 C10orf81 11080 0 82276 83362 0.00148522 8 0 chr10 1 115531012 115542192 219857_at 115508037 115519932 GUCA2A 0 12975 127841 18697 0.001489389 50 100 chr1 −1 42628362 42630389 207003_at 42502000 42631368 MATN2 12519 380486 557256 1 0.001516526 100 100 chr8 1 98881311 99047940 202350_s_at 98893830 99036276 C2orf15 29140 14379 40714 0 0.001531965 0 0 chr2 1 99757948 99767950 1552740_at 99562157 99728808 SLC39A5 28709 510113 6484 5472 0.001534757 75 100 chr12 1 56623847 56631630 1552281_at 56652556 56659940 COL8A1 0 570008 0 179295 0.001535013 17 0 chr3 1 99357319 99518070 226237_at 98620955 99531832 SATB2 37318 0 11387 0 0.001539121 100 100 chr2 −1 200134223 200322819 213435_at 200360137 200523461 CES2 18044 214137 40796 0 0.001557981 83 100 chr16 1 66968363 66978999 209668_x_at 66940239 66950319 NKAIN2 8658 0 0 0 0.001591582 17 0 chr6 1 124125286 125146803 242002_at 123321699 124116628 CWH43 563 0 80364 0 0.001665747 88 100 chr4 1 48988264 49064096 220723_s_at 48988827 49138512 NRXN3 0 0 684659 627586 0.001684009 8 0 chr14 1 79117568 80328307 205795_at 78447748 79745133 CDC45 51839 113019 43833 0 0.001694424 96 0 chr22 1 19466982 19508135 204126_s_at 19518821 19699558 C11orf82 76157 93378 105251 12886 0.001696204 75 0 chr11 1 82625731 82645697 228281_at 82453054 82549574 KLK8 0 0 15491 957 0.001744371 8 0 chr19 −1 51499264 51504958 206125_s_at 51416341 51518249 PARVB 7238 106423 24533 2421 0.001764143 0 0 chr22 1 44395091 44564803 37966_at 44402329 44414770 EPB41L3 7072 0 1 0 0.001821533 58 100 chr18 −1 5392383 5544241 206710_s_at 5301384 5537169 SLC6A6 578 110921 590 0 0.001821533 25 0 chr3 1 14444076 14530857 205920_at 14444654 14452211 TRPM2 5692 15527 0 10520 0.001827718 21 0 chr21 1 45770046 45862964 205708_s_at 45775738 45829179 PFN2 7485 818415 1077 0 0.001842406 100 100 chr3 −1 149682691 149688896 204992_s_at 149696381 149956030 METTL7A 15852 905200 249298 81609 0.001866301 100 100 chr12 1 51318534 51326300 207761_s_at 51222303 51302682 SLC35E4 350 111638 93435 0 0.001877575 50 0 chr22 1 31031639 31043880 1568623_a_at 31020352 31031289 LMCD1 13641 68392 265740 0 0.001883614 29 0 chr3 1 8543393 8609805 218574_s_at 8557034 8619335 ITM2A 0 0 967161 967865 0.001894732 92 100 chrX −1 78615881 78622856 202746_at 77395364 78853597 IL33 58636 0 170466 170672 0.001913861 88 8 chr9 1 6241682 6257983 209821_at 6019920 6183046 LDLRAD3 3286 567797 18139 15 0.001913861 8 0 chr11 1 35965628 36253686 234985_at 35838203 35962342 OTUB2 110 102476 627 0 0.00191985 29 0 chr14 1 94492724 94515276 219369_s_at 94439878 94492614 COL1A1 65 0 83795 0 0.00194236 12 0 chr17 −1 48260650 48278993 202311_s_at 48279058 48350325 ORC1L 17988 947282 147164 0 0.001943513 46 0 chr1 −1 52838501 52870131 205085_at 52888119 52983719 DPEP1 19757 435809 62 17221 0.001950809 83 0 chr16 1 89696691 89704864 205983_at 89665675 89676934 SLC7A11 13988 1242952 1036798 318232 0.001962998 83 8 chr4 −1 139085251 139163503 217678_at 139177491 139929775 SEMA6D 39235 92023 458933 0 0.001994059 88 100 chr15 1 48010686 48066417 226492_at 47932866 47971451 HOMER1 6148 204205 97600 0 0.00199715 25 0 chr5 −1 78668459 78810040 213793_s_at 78816188 78902854 FST 6188 821995 492479 0 0.002000986 0 0 chr5 1 52776239 52782964 226847_at 52782427 52847175 WDHD1 92088 846453 859 0 0.002013991 33 0 chr14 −1 55405668 55493795 204728_s_at 55585883 55595666 CYB5R2 4230 0 161206 0 0.002028451 62 0 chr11 −1 7686326 7694821 220230_s_at 7699051 8008893 DAPL1 0 0 175754 173026 0.002039682 21 0 chr2 1 159651829 159672505 229290_at 159537049 159766248 GABRB2 1772 0 300190 1044 0.002054068 38 12 chr5 −1 160715436 160973649 242344_at 160975421 162777424 CNTN3 0 137020 92114 93216 0.002108873 83 100 chr3 −1 74311719 74570291 229831_at 73680359 74663468 MRPS21 14016 512912 0 188 0.002172338 92 100 chr1 1 150266289 150281414 222997_s_at 150280305 150293469 PROX1 25455 0 198574 444 0.002188037 79 8 chr1 1 214161860 214214596 229376_at 214119835 214136405 CENPI 28109 2081 1024583 2149 0.00219666 33 0 chrX 1 100355426 100418670 214804_at 100322117 100327317 TSPAN7 4606 0 270817 0 0.002203838 100 100 chrX 1 38420623 38548167 202242_at 38224466 38416017 C2orf70 398 0 57679 0 0.002205452 12 0 chr2 1 26785450 26802400 231126_at 26726754 26785052 FZD3 9953 0 130703 0 0.002234066 12 0 chr8 1 28351773 28431788 219683_at 28335606 28341820 MCM10 48555 103559 109128 0 0.002297013 38 0 chr10 1 13203554 13253104 222962_s_at 13142558 13154999 RBM11 75 0 188490 0 0.002297137 0 0 chr21 1 15588499 15600693 232549_at 15436705 15588424 TRIM29 5142 0 98850 152 0.002321878 54 0 chr11 −1 119981983 120008863 211002_s_at 120014005 120039592 NOTUM 16275 1453763 17271 0 0.00235196 21 0 chr17 −1 79910388 79919169 228649_at 79897558 79902894 TFAP2A 16995 0 1617 151 0.002379161 25 0 chr6 −1 10396916 10415470 204653_at 10432465 10690667 C1orf21 13835 962814 181815 0 0.002389438 100 100 chr1 1 184356192 184598154 223125_s_at 184051705 184342357 CEACAM7 11681 0 120452 156380 0.002391996 100 100 chr19 −1 42177235 42192296 206198_s_at 42168674 42180615 UNC5CL 698 0 0 10686 0.00239258 58 0 chr6 −1 40994772 41006928 231008_at 41007626 41015478 PKIA 0 10890 0 98 0.002409055 8 0 chr8 1 79428336 79515485 204612_at 77921809 79428387 GALNT12 40725 79801 25166 0 0.002417303 100 100 chr9 1 101569981 101612363 218885_s_at 101610706 101698371 PTP4A3 6191 28812 95970 3655 0.002489148 58 0 chr8 1 142432007 142441620 206574_s_at 142438198 142528142 2926 252659 10711 3406 0.002527591 79 0 chr6 1 31674681 31685695 207457_s_at 31677607 31688229 REEP1 2617 0 141400 0 0.002541043 8 0 chr2 −1 86441116 86564777 204365_s_at 86567394 86601683 FPR1 0 0 32167 31941 0.002554978 4 0 chr19 −1 52249027 52255150 205119_s_at 52231520 52381753 SLC28A3 0 0 328881 199897 0.002657296 4 0 chr9 −1 86890372 86955598 220475_at 86933053 87278151 PVRL3 7338 266721 1013140 0 0.002657296 96 100 chr3 1 110790590 110854801 213325_at 110621522 110783252 SLC4A11 10931 416811 0 0 0.002667872 4 0 chr20 −1 3208063 3218812 223748_at 3229743 3381098 C10orf81 11080 0 82276 83362 0.002669553 12 0 chr10 1 115531012 115542192 1554190_s_at 115508037 115519932 REG3A 0 0 165703 166286 0.002707981 54 17 chr2 −1 79384132 79386879 205815_at 79220617 79739679 ADAMTS2 5556 65010 0 0 0.002708834 4 0 chr5 −1 178537852 178772385 226311_at 178777941 178949264 SLC38A5 13368 13508 396184 5665 0.002713218 83 0 chrX −1 48316920 48328565 234973_at 48286581 48315197 BAG2 18242 274918 48321 0 0.002737327 38 12 chr6 1 57037124 57049735 209406_at 57055366 57077011 PQLC3 0 337052 686 62 0.002754994 100 100 chr2 1 11295498 11319000 225579_at 11055610 11295549 CDKN2B 4209 0 3285 0 0.002768858 62 100 chr9 −1 22002902 22009280 236313_at 22013489 22435022 ADH4 0 275530 803300 55318 0.002805008 33 4 chr4 −1 100044818 100065448 231678_s_at 100019863 100066623 LGR5 68682 0 316400 0 0.002805793 96 0 chr12 1 71833813 71978622 210393_at 71715727 71765131 PDE10A 6449 335577 0 0 0.002827076 0 0 chr6 −1 165740776 166075588 205501_at 163846971 166069139 TEAD2 3186 22475 21505 23 0.002839581 62 0 chr19 −1 49843857 49865714 226408_at 49868900 49924222 NPTX2 7167 0 0 0 0.002857438 17 8 chr7 1 98246609 98259180 213479_at 98253776 98462956 RBPMS 5020 428515 302946 0 0.002878689 46 0 chr8 1 30241944 30429734 207836_s_at 30056395 30236924 KIAA0895 114 83742 1078 0 0.002880769 4 0 chr7 −1 36363830 36429734 213424_at 36429848 36443570 REN 0 152072 31966 14340 0.00288615 29 0 chr1 −1 204123947 204135450 206367_at 204133982 204159320 HOXA10 40252 0 9331 0 0.002898676 100 100 chr7 −1 27202057 27205129 209905_at 27245381 27250842 PROX1 24881 0 199148 0 0.002908057 83 8 chr1 1 214161286 214209282 207401_at 214119835 214136405 FXYD3 5468 10995 109288 8247 0.002928236 100 100 chr19 1 35607166 35615227 202489_s_at 35532020 35601698 HPGD 29020 0 897 211 0.002991419 100 100 chr4 −1 175411328 175444049 203914_x_at 175473069 175750280 DUOXA2 7716 0 14639 0 0.002999027 83 8 chr15 1 45406519 45410619 230615_at 45360487 45398803 PLAU 17455 550920 266454 0 0.003050955 42 12 chr10 1 75670915 75677255 205479_s_at 75635405 75653460 SEC16B 23333 178344 464015 15109 0.003071079 21 0 chr1 −1 177898955 177991722 1552880_at 178015055 178026664 COL12A1 6612 0 518 0 0.003085838 29 0 chr6 −1 75794042 75915767 231879_at 75795161 75909155 EPB41L3 7072 0 1 0 0.003096029 29 100 chr18 −1 5392383 5544241 212681_at 5301384 5537169 GRAMD2 8017 202811 34876 16 0.003103196 0 0 chr15 −1 72452148 72490136 229616_s_at 72476997 72482119 TBX3 24750 0 2373 0 0.003144084 96 0 chr12 −1 115108059 115121969 229576_s_at 115146719 115165673 FADS1 18815 221038 10149 0 0.003163942 4 0 chr11 −1 61567099 61584463 208962_s_at 61603278 61658533 EPHB1 9320 0 0 0 0.00316428 0 0 chr3 1 134514104 134979309 230425_at 134523424 135675199 PCDH7 7610 0 0 0 0.003194669 0 0 chr4 1 30722037 30733590 205534_at 27027813 30714427 WDHD1 92088 846453 859 0 0.003201735 8 0 chr14 −1 55405668 55493795 204727_at 55585883 55595666 HGF 0 1062718 672168 158638 0.003204291 4 0 chr7 −1 81372007 81399347 210997_at 81084866 82065278 PCK1 20626 0 0 35885 0.003208323 92 100 chr20 1 56136136 56141513 208383_s_at 56156762 56182232 HIBADH 261 179138 653 0 0.003210374 100 100 chr7 −1 27565061 27702614 224812_at 27702875 27718744 KITLG 39939 1538368 4325 0 0.003210374 100 100 chr12 −1 88886566 88974238 226534_at 89014177 89032174 GPR110 17758 0 33938 266357 0.003210374 17 0 chr6 −1 46965440 47010099 238689_at 46821624 46992341 KANK1 207 0 33014 0 0.003216108 100 100 chr9 1 470291 746105 213005_s_at 215466 470084 DIAPH3 5832 24008 309923 0 0.003217707 25 0 chr13 −1 60239717 60737992 232596_at 60743824 60965589 SKAP2 2048 229114 230564 0 0.003230505 92 100 chr7 −1 26706681 26904362 204362_at 26906410 27124857 PLAU 17455 550920 266454 0 0.003254959 54 8 chr10 1 75670915 75677255 211668_s_at 75635405 75653460 ERCC6L 39022 54379 326940 0 0.003263889 58 0 chrX −1 71424510 71458897 219650_at 71497919 71515951 C10orf99 16995 0 2088807 20706 0.003263889 100 100 chr10 1 85933494 85945050 227735_s_at 85905537 85916499 SCAND3 8892 0 0 0 0.003293145 4 4 chr6 −1 28539405 28555112 244758_at 28517288 28546220 ALDH1L1 8694 0 0 0 0.003352198 71 8 chr3 −1 125822414 125898762 205208_at 125907456 125925541 KRT17 0 4354 109288 23912 0.003353993 12 0 chr17 −1 39775689 39780829 212236_x_at 39711383 39800097 NRXN3 424 55406 1312745 0 0.003363152 29 4 chr14 1 79745654 80330758 229649_at 79746078 81177275 SSBP2 5703 167173 101368 0 0.003368706 12 96 chr5 −1 80708840 81047072 203787_at 80695952 81041369 CXCL14 10624 0 0 0 0.003412183 100 100 chr5 −1 134906376 134914754 222484_s_at 134885256 134904130 OSR2 22376 950424 0 97 0.003412303 17 0 chr8 1 99960401 99964332 213568_at 99872825 99938025 SLC22A3 16044 0 1247 0 0.003446418 54 0 chr6 1 160769300 160873613 205421_at 160746813 160753256 BNIP3 9283 14576 0 0 0.003472643 38 0 chr10 −1 133781578 133795435 201848_s_at 133804718 133843600 RPL39L 8168 170035 0 0 0.003495557 29 0 chr3 −1 186838736 186857272 210115_at 186801434 186849104 DPYSL2 4669 31326 64311 0 0.003543874 100 100 chr8 1 26435410 26515694 200762_at 26379928 26430741 SYT13 15714 0 835 0 0.003551455 100 100 chr11 −1 45261853 45307884 226086_at 45323598 45677905 MPP1 13827 0 1120290 0 0.003552925 75 100 chrX −1 154006959 154033796 202974_at 154047623 154060810 TAF8 33772 366228 127288 0 0.003585984 0 0 chr6 1 42018251 42025527 229412_at 42052023 42066504 HPGD 29020 0 897 211 0.003598904 100 100 chr4 −1 175411328 175444049 211548_s_at 175473069 175750280 CKAP2L 13381 131276 331756 0 0.00365173 71 0 chr2 −1 113494184 113522254 229610_at 113535635 113544577 TSPAN5 5138 448802 1288968 0 0.003652172 46 0 chr4 −1 99391518 99579780 209890_at 99567766 99574642 LRRC2 53418 93043 234 233 0.00366087 17 0 chr3 −1 46556913 46608040 219949_at 46521837 46554622 HSPA4L 1457 312425 52403 0 0.003687998 62 0 chr4 1 128702976 128754197 205543_at 128632751 128701519 SIM2 13424 0 955 0 0.003704607 8 0 chr21 1 38071434 38122218 206558_at 37854364 38058010 KLHL13 7956 0 2781970 6 0.003739396 17 46 chrX −1 117031776 117250761 227875_at 117106826 117242805 DNAJC12 2849 77859 492612 11624 0.003743751 8 0 chr10 −1 69570966 69597854 223722_at 69574994 69595005 GGCT 611 149016 27028 0 0.003748202 100 100 chr7 −1 30536237 30544460 215380_s_at 30545071 30559850 HSPA2 53719 287625 3196 4252 0.003845752 100 100 chr14 1 65002623 65009955 211538_s_at 65056342 65079340 KRT7 44630 76780 0 0 0.003873112 33 0 chr12 1 52626954 52642709 209016_s_at 52671584 52701887 AQP3 1990 242392 62813 0 0.003898169 100 100 chr9 −1 33441152 33447609 39248_at 33379626 33445619 CHST3 6059 164128 751 0 0.003934905 0 0 chr10 1 73724123 73773322 209834_at 73649045 73718064 IL22 0 33550 1078651 78564 0.003952088 0 0 chr12 −1 68642025 68647284 222974_at 68214442 68689811 ALDH1A1 0 0 474142 587226 0.003964488 100 100 chr9 −1 75515578 75567971 212224_at 75457522 75752046 NPW 48936 89521 27719 198 0.004034202 46 0 chr16 1 2069521 2070755 243110_x_at 2015477 2020585 C3orf70 15242 346505 805 0 0.00403475 100 100 chr3 −1 184795838 184870802 242447_at 184886044 184907969 IRAK1 84219 38624 371925 0 0.004051199 100 100 chrX −1 153275951 153285431 201587_s_at 153369650 153421858 TRIM7 17180 0 16352 0 0.004060682 54 0 chr5 −1 180630118 180632293 223694_at 180608872 180615113 HIGD1A 12070 39063 30766 0 0.004061557 96 100 chr3 −1 42824404 42845934 242317_at 42858004 42922198 AZGP1 0 21715 0 21427 0.004128575 71 4 chr7 −1 99564353 99573780 217014_s_at 99559725 99587874 SPP1 0 35842 31363 31662 0.004147984 42 29 chr4 1 88896819 88904562 209875_s_at 88397786 88924190 POLH 2218 271864 889 0 0.004148482 42 0 chr6 1 43543887 43583397 1557701_s_at 43546105 43556976 KLHL32 125 0 907481 0 0.004173878 0 0 chr6 1 97372605 97588630 1553765_a_at 97372730 97587856 SMOC2 4622 0 63315 0 0.004174854 62 100 chr6 1 168841831 169068674 223235_s_at 168783231 168837209 AXIN2 8092 78226 15167 0 0.00427155 100 0 chr17 −1 63524685 63557765 224176_s_at 63519783 63549673 BEX4 7464 0 339 0 0.004274184 71 100 chrX 1 102470020 102472174 215440_s_at 102196004 102462556 HOXA7 49085 2820 9620 0 0.004282668 75 96 chr7 −1 27193346 27196296 235753_at 27245381 27250842 LPAR1 3875 1350143 1948 0 0.004336624 79 100 chr9 −1 113635543 113800323 204036_at 113804198 114122387 CBR3 6229 29079 23074 0 0.004357415 54 0 chr21 1 37507210 37518864 205379_at 37495606 37500981 SAA2 0 0 141879 39275 0.004362905 12 0 chr11 −1 18266787 18270182 214456_x_at 18127733 18275128 MNS1 12444 25374 98230 0 0.004380081 54 0 chr15 −1 56720929 56757335 219703_at 56769779 56928295 HOXA5 58606 0 0 0 0.004380081 71 100 chr7 −1 27180671 27183463 213844_at 26906410 27124857 NR5A2 5318 0 6748 7745 0.004423695 83 100 chr1 1 199996730 200146552 210174_at 199963808 199991412 BDNF 9780 0 0 0 0.004428973 0 0 chr11 −1 27676440 27743605 206382_s_at 27753385 28035841 FXYD3 5468 10995 109288 8247 0.004428973 100 100 chr19 1 35607166 35615227 202488_s_at 35532020 35601698 TRIM7 17059 0 16473 0 0.004439342 17 0 chr5 −1 180620924 180632172 239694_at 180608872 180615113 DRP2 0 0 905251 28020 0.004443074 4 0 chrX 1 100474758 100519486 1556627_at 100405981 100558831 ARHGAP11A 46368 214982 145634 0 0.00444838 17 0 chr15 1 32907691 32932150 204492_at 32855210 32861323 SERPINA1 2908 3274 206743 215325 0.004450684 58 0 chr14 −1 94843084 94856974 230318_at 94641762 94854066 PHLDA1 48055 741822 731051 0 0.004496546 100 0 chr12 −1 76419227 76425556 217997_at 76344741 76377501 MND1 72580 305250 95023 0 0.004496662 92 8 chr4 1 154265801 154336270 223700_at 154338381 154379219 CYP27B1 78118 0 2427 975 0.004508014 0 0 chr12 −1 58156118 58160976 205676_at 58030134 58082858 C10orf99 16995 0 2088807 20706 0.004545862 100 100 chr10 1 85933494 85945050 227736_at 85905537 85916499 CNTNAP3 104064 0 665225 0 0.004552087 0 0 chr9 −1 39072764 39288135 223796_at 39052051 39184071 SERPINB3 0 0 275098 238839 0.004559531 8 0 chr18 −1 61322431 61329197 209719_x_at 61174562 61603221 PCP4 0 0 254344 276995 0.00457272 33 0 chr21 1 41239243 41301322 205549_at 41035457 42212925 SESN1 60269 192557 1006 0 0.00457387 100 100 chr6 −1 109307645 109330751 218346_s_at 109256128 109270482 GALNT1 65177 71479 295199 72259 0.004579726 100 100 chr18 1 33234524 33291798 201722_s_at 33299701 33526942 PCDHB15 14067 0 75058 1464 0.004601108 0 0 chr5 1 140624981 140627742 231789_at 140639048 140655207 PHLDA1 48055 741822 731051 0 0.00463039 46 0 chr12 −1 76419227 76425556 218000_s_at 76344741 76377501 VPS4B 3152 29328 514602 0 0.004643759 100 100 chr18 −1 61056423 61089693 218171_at 61092845 61122314 PDGFRB 1459 0 33853 10605 0.004718827 0 0 chr5 −1 149493400 149535423 202273_at 149511810 149533964 DEFA1 0 0 269575 111748 0.004733051 4 0 chr8 −1 6835172 6837602 205033_s_at 6701491 6988157 TNFRSF10C 11022 216376 0 0 0.00475574 25 0 chr8 1 22960432 22974950 211163_s_at 22942117 22949410 LCN15 8214 371215 10045 3810 0.00475574 75 4 chr9 −1 139654086 139658965 1569532_a_at 139667179 139674915 DNAH14 308 14006 311502 0 0.00475574 54 0 chr1 1 225117384 225212306 242283_at 224812470 225117076 C7orf30 69 464657 49983 0 0.004772303 100 100 chr7 1 23338819 23351348 226385_s_at 23287523 23338750 RLN2 0 0 1107179 492 0.004782597 0 0 chr9 −1 5299868 5304969 214519_s_at 5135871 5359217 GMPR 3068 126785 41358 0 0.004785154 8 0 chr6 1 16238807 16295417 204187_at 16241875 16300322 KCNJ8 59018 39013 165933 116980 0.004810307 0 0 chr12 −1 21917889 21927747 205304_s_at 21986765 22093905 CMBL 103137 211137 33849 224 0.004811555 100 100 chr5 −1 10279389 10308138 227522_at 10178498 10205001 IL17RD 7797 145558 793989 24 0.004811555 42 0 chr3 −1 57124010 57199403 227997_at 57207200 57253382 TXNL1 29870 403083 713517 0 0.004815834 100 100 chr18 −1 54264439 54305920 201588_at 53453587 54276050 WDR4 46030 52709 194889 0 0.004822918 42 0 chr21 −1 44263204 44299641 226882_x_at 44232396 44253611 RPGRIP1L 104649 115271 269831 0 0.004877379 21 0 chr16 −1 53633824 53737771 213959_s_at 53540989 53633122 MAGEA2B 10 3745 76144 15620 0.004877379 0 0 chrX 1 151883090 151887096 1553830_s_at 151883100 151948085 SLC2A1 8398 47087 49663 0 0.004914882 62 71 chr1 −1 43391519 43424501 201250_s_at 43401524 43416103 OTUB2 110 102476 627 0 0.004914882 33 0 chr14 1 94492724 94515276 222878_s_at 94439878 94492614 MAOA 94610 0 3422165 0 0.004926885 100 100 chrX 1 43515467 43606068 204388_s_at 43202978 43420857 NR3C1 5153 816543 515 0 0.00493573 29 100 chr5 −1 142657496 142783265 216321_s_at 142609282 142778112 IGFBP5 5281 1391508 229 763 0.004969324 17 0 chr2 −1 217536828 217560248 211958_at 217565529 218843435 MNAT1 18597 171232 1829 10707 0.004983683 0 0 chr14 1 61201480 61436671 203565_s_at 61128150 61182883 WDR12 10314 974807 39754 0 0.004993019 100 100 chr2 −1 203745323 203776949 218512_at 203787263 203833499 SLC16A7 0 179392 1749500 92618 0.005016111 42 92 chr12 1 60083126 60175407 207057_at 59990530 62574045 C13orf18 164 10379 1112 0 0.005023906 100 100 chr13 −1 46917099 46961621 44790_s_at 46961785 46974863 ANGPT2 42076 168337 0 3286 0.00505811 4 0 chr8 −1 6357172 6420930 211148_s_at 6463006 6468475 MAGEA2B 10 3745 76144 15620 0.005068014 4 0 chrX 1 151883090 151887096 214603_at 151883100 151948085 SMOC2 4622 0 63315 0 0.005076311 12 0 chr6 1 168841831 169065106 243946_at 168783231 168837209 MUCL1 0 0 304264 265707 0.005086226 0 0 chr12 1 55248299 55252170 1553602_at 54982626 56039891 ALDH1A3 8795 0 766 0 0.005086226 58 67 chr15 1 101419581 101456831 203180_at 101396316 101410786 STK31 0 53690 32 29108 0.005090232 4 0 chr7 1 23749786 23872132 223883_s_at 23735576 23771279 VSNL1 64090 0 3072 0 0.005118909 88 12 chr2 1 17720393 17837345 203798_s_at 16689858 17656303 LEMD1 0 0 33330 33648 0.005143478 4 0 chr1 −1 205350506 205391182 229927_at 205321228 205399229 ARMC10 43100 167437 74969 0 0.005165251 100 100 chr7 1 102715328 102740205 1554480_a_at 102667148 102672228 C16orf46 20137 71682 19755 0 0.005189253 4 0 chr16 −1 81087102 81110818 230281_at 81130955 81268589 KCNH8 5094 0 2261718 0 0.005198671 8 0 chr3 1 19189946 19577138 1552742_at 18493624 19184852 GALNT12 40725 79801 25166 0 0.005226977 100 100 chr9 1 101569981 101612363 222773_s_at 101610706 101698371 SSX2IP 7856 291185 201941 0 0.005226977 17 0 chr1 −1 85109390 85156228 210871_x_at 85164084 85353693 FAM131B 44849 109966 16747 0 0.005288211 8 0 chr7 −1 143050493 143059845 205368_at 143104694 143110401 DIO2 0 47592 739972 349508 0.005293947 4 0 chr14 −1 80664089 80677840 203700_s_at 79746078 81177275 F2RL2 0 75014 196847 91862 0.005303581 50 0 chr5 −1 75911328 75919259 230147_at 75704188 76002246 WISP1 0 452493 31774 105017 0.00531349 0 0 chr8 1 134203312 134241569 235821_at 134138989 134219769 NEFL 8077 0 0 324 0.005319168 12 0 chr8 −1 24808468 24814624 221805_at 24822701 24846167 MUM1L1 0 0 345067 345187 0.005348525 0 0 chrX 1 105412298 105452949 229160_at 105078443 105854952 ASCL2 3141 0 3602 0 0.00534907 100 83 chr11 −1 2289725 2292182 229215_at 2282737 2289041 ABHD6 13918 0 59807 0 0.005386873 75 100 chr3 1 58223233 58280459 221552_at 58168892 58209315 KHDRBS3 2801 0 792549 0 0.005428065 92 96 chr8 1 136469700 136659838 209781_s_at 135846364 136466899 NEB 0 0 324944 93475 0.005534664 4 0 chr2 −1 152341850 152591001 205054_at 152462337 152632425 PHF19 42431 530714 1410 0 0.005543562 71 0 chr9 −1 123631865 123639466 227211_at 123588593 123597035 PM20D2 2177 37513 27542 0 0.005545656 100 100 chr6 1 89855769 89875284 225421_at 89844813 89853592 CFD 819 470664 11788 853 0.005571608 100 100 chr19 1 859665 863606 205382_s_at 848149 858846 LFNG 4598 443999 1994 0 0.00560566 100 100 chr7 1 2559476 2568063 228762_at 2564074 2572016 PSPH 74712 53210 27835 0 0.005610634 38 0 chr7 −1 56078760 56119297 205194_at 56194009 56238727 TCF12 2967 348114 30231 0 0.0056393 100 100 chr15 1 57210823 57582051 208986_at 57185279 57207856 NAT6 66135 68166 16171 0 0.005674819 88 4 chr3 −1 50333883 50336831 210619_s_at 50402966 50540137 JUB 2044 251690 2398 0 0.005679632 8 0 chr14 −1 23440383 23451851 225807_at 23440519 23449807 ESCO2 41076 62011 160178 0 0.005685292 62 4 chr8 1 27632071 27662742 235588_at 27549414 27590995 B3GNT6 0 763082 4259 5258 0.005685292 79 88 chr11 1 76745435 76753003 1552833_at 76733720 76753433 67105 35285 457334 0 0.005688368 12 0 chr16 1 20817785 20860990 215215_s_at 20884890 20897335 TMEM71 0 22095 86054 14528 0.005762863 75 17 chr8 −1 133722194 133772914 238429_at 133739160 133781519 SMPDL3A 892 57987 206357 0 0.00577302 100 100 chr6 1 123110315 123130865 213624_at 122931724 123109423 ANGPT2 42076 168337 0 3286 0.005783769 8 0 chr8 −1 6357172 6420930 205572_at 6463006 6468475 RGMB 12354 217102 78532 0 0.005789055 83 79 chr5 1 98104999 98132198 227339_at 97979164 98092645 HAUS6 27324 133116 1424 6 0.005801603 0 0 chr9 −1 19053141 19103117 218602_s_at 19130441 19142908 MB 0 373502 32847 65506 0.005815531 96 100 chr22 −1 36002811 36013503 204179_at 35937556 36034465 SFXN3 12433 29020 17300 0 0.005844456 25 0 chr10 1 102790991 102800998 220974_x_at 102773407 102778558 ARNT2 5356 23746 0 0 0.005859934 12 0 chr15 1 80696692 80890269 202986_at 80549855 80691336 ITPK1 3461 182015 13120 0 0.005935433 100 100 chr14 −1 93407054 93582263 210740_s_at 93585724 93597102 PRIM2 3769 132439 93977 92291 0.005940743 17 0 chr6 1 57179603 57191161 1554885_a_at 57138323 57175834 MEP1A 0 0 142666 57810 0.005945543 100 100 chr6 1 46761127 46807515 206000_at 46708815 46761211 C12orf66 10369 67663 167822 0 0.005972623 0 0 chr12 −1 64581359 64616071 1554068_s_at 64626440 64778018 RRM2B 36911 40521 154213 135 0.005989519 83 100 chr8 −1 103216732 103251346 223342_at 103136798 103214435 AQP3 1990 242392 62813 0 0.005993406 12 0 chr9 −1 33441152 33447609 39249_at 33379626 33445619 RBPMS 5020 428515 302946 0 0.006039127 96 100 chr8 1 30241944 30405027 209487_at 30056395 30236924 POLR3G 28075 53539 804435 0 0.006093044 33 0 chr5 1 89770706 89810370 206653_at 89711697 89742631 CEACAM7 11681 0 120452 156380 0.006112623 100 100 chr19 −1 42177235 42192296 211848_s_at 42168674 42180615 MCM4 27413 243954 552986 0 0.006122886 83 0 chr8 1 48873494 48890068 212141_at 48900907 48917534 FRZB 4855 399866 256110 0 0.006122886 92 100 chr2 −1 183698002 183731890 203697_at 183645523 183727035 CHFR 9151 454256 0 0 0.006177685 17 33 chr12 −1 133416938 133464184 223931_s_at 133408647 133455033 PLCE1 40899 160558 34595 36367 0.006221938 100 100 chr10 1 95790569 96088146 205111_s_at 95693652 95749670 CTTNBP2 17317 9204 912 0 0.006221992 88 25 chr7 −1 117350705 117513561 232136_s_at 117460302 117496244 DCN 0 193541 221247 224232 0.006222875 100 100 chr12 −1 91539036 91572329 201893_x_at 90355184 91783891 PTPRN2 26628 0 17535 0 0.006300279 83 79 chr7 −1 157331750 158380480 203030_s_at 158307672 158353852 ZNF511 32126 168032 10778 13 0.006311751 92 0 chr10 1 135121979 135126662 225307_at 135075469 135089853 FIGNL1 15639 24459 227 0 0.006315512 79 0 chr7 −1 50511831 50518048 1552921_a_at 50411178 50502409 FAM46C 7420 330078 3265 0 0.006339909 100 100 chr1 1 118148556 118170994 226811_at 118118373 118141136 RUNX1 72946 202856 217967 0 0.006361713 100 100 chr21 −1 36160098 36260987 209360_s_at 36333933 36366356 TNFRSF11B 275 186437 254731 7 0.006361899 100 67 chr8 −1 119935797 119964383 204933_s_at 119964658 120167597 FANCI 6706 91817 116018 0 0.006370144 96 38 chr15 1 89787180 89860492 213007_at 89745309 89780474 FAM55D 169059 0 153769 155897 0.006375204 100 100 chr11 −1 114441314 114466484 220645_at 114635543 115368482 ALDH4A1 1773 51861 1615 0 0.006382891 0 0 chr1 −1 19197926 19229275 211552_s_at 19220360 19227502 PTGS2 276 433823 1362224 0 0.006383418 50 12 chr1 −1 186640923 186649555 204748_at 186400111 186649279 SLITRK6 0 38377 1915741 1919725 0.00642599 100 100 chr13 −1 86366925 86373623 232176_at 84465407 86760270 TNFRSF17 6954 613536 61867 11294 0.006435719 88 100 chr16 1 12058964 12061925 206641_at 12029195 12052010 EXO1 4705 38104 423412 0 0.006435719 88 0 chr1 1 242011482 242053241 204603_at 241811234 242006777 OXGR1 3922 0 695 0 0.006477776 75 0 chr13 −1 97637973 97646604 1553319_at 97594765 97642682 LRRC8E 1865 99389 14093 0 0.006484922 8 0 chr19 1 7953390 7966906 239433_at 7946329 7951525 AHNAK2 10172 35738 45285 0 0.006490786 12 8 chr14 −1 105403591 105444694 212992_at 105404695 105434522 ORM1 0 174844 64246 74804 0.006492246 4 0 chr9 1 117085336 117088755 205041_s_at 116925630 117094770 FMO3 0 26641 425601 394500 0.00652394 0 0 chr1 1 171060018 171086959 40665_at 170873486 171302735 ADAMTS9 10154 121285 2226 0 0.006534678 12 0 chr3 −1 64501490 64673676 1554697_at 64683830 65328910 PMAIP1 9473 181841 202782 0 0.006554339 83 50 chr18 1 57567180 57571538 204286_s_at 57576653 58987404 RARRES1 54613 106822 161139 0 0.006565659 100 100 chr3 −1 158414681 158450485 221872_at 158505098 158516616 APLF 5396 38196 1717 0 0.006567242 0 0 chr2 1 68694693 68807294 241379_at 68700089 68870315 TLR4 46892 0 288376 40618 0.00658545 67 0 chr9 1 120466610 120478053 232068_s_at 120183010 120419718 PTPRN2 26628 0 17535 0 0.006586901 8 0 chr7 −1 157331750 158380480 211534_x_at 158307672 158353852 UGT2A3 203785 0 1237673 601587 0.00659923 71 100 chr4 −1 69794181 69817509 219948_x_at 69587469 69613724 GGT6 3019 50624 20116 4891 0.006618473 100 100 chr17 −1 4460224 4463876 236225_at 4466895 4476679 CLCN4 46290 14977 1424365 1297 0.006620275 0 0 chrX 1 10125024 10205700 205148_s_at 10171314 10410830 TFPI 0 226612 663709 664298 0.006670769 71 100 chr2 −1 188328957 188378368 213258_at 187714106 189156378 ABHD2 0 222408 1331 142 0.006675411 100 100 chr15 1 89631405 89745591 225337_at 89625750 89631521 EDNRA 4870 421533 0 115 0.006697313 0 0 chr4 1 148402084 148466106 216235_s_at 148406954 148533951 INHBA 0 660770 183342 2473 0.006702605 8 0 chr7 −1 41724712 41742706 210511_s_at 40180732 41744986 WHSC1 100147 115631 105661 20585 0.006750952 33 0 chr4 1 1894572 1983934 209054_s_at 1769186 1794425 CSPP1 26760 350844 640 0 0.006825026 0 0 chr8 1 67976603 68108494 1554873_at 67941025 67949843 RPL7L1 16688 354650 10177 10797 0.006851352 100 100 chr6 1 42847373 42857634 225515_s_at 42864061 42879234 GCSH 947 52492 565 0 0.00685861 100 100 chr16 −1 81115566 81130008 213129_s_at 81130955 81268589 FRZB 4855 399866 256110 0 0.006909155 79 100 chr2 −1 183698002 183731890 203698_s_at 183645523 183727035 WDHD1 92088 846453 859 0 0.006921728 17 0 chr14 −1 55405668 55493795 216228_s_at 55585883 55595666 KLK12 0 0 17019 2672 0.006924307 29 0 chr19 −1 51532348 51538148 234316_x_at 51523889 51568096 RGS20 0 166920 10002 8258 0.006968335 4 0 chr8 1 54764368 54871861 210138_at 54758387 54783035 SMARCA1 10854 0 1534744 70 0.006980988 8 0 chrX −1 128580482 128657477 215294_s_at 125623341 128646623 BEX2 3672 0 95279 0 0.006993088 50 96 chrX −1 102564274 102565974 224367_at 102485299 102562302 CHEK1 59968 69755 129286 198 0.006993088 92 58 chr11 1 125495036 125525640 205394_at 125555004 125751240 SESN3 11213 0 78834 0 0.006993884 46 0 chr11 −1 94906133 94964246 235683_at 94887006 94953033 ASNS 6214 20622 87822 0 0.006993884 100 100 chr7 −1 97481440 97501443 205047_s_at 97507657 97556859 APCDD1 4839 234624 271377 0 0.00701885 100 96 chr18 1 10454625 10488698 225016_at 10139155 10449786 PCSK1 0 0 0 0 0.00701885 79 42 chr5 −1 95726119 95768984 205825_at 95680613 95991182 ALPK3 46220 339086 548054 282 0.007043138 17 0 chr15 1 85359911 85416713 214846_s_at 85406131 85454098 RAP1GAP 4403 0 144855 0 0.007043647 100 100 chr1 −1 21922714 21995799 203911_at 21986130 21991396 TFDP1 1421 597056 1616 18434 0.007056944 100 100 chr13 1 114239056 114295504 212330_at 114186307 114237635 BBS5 0 33933 115599 194 0.007118082 0 0 chr2 1 170335688 170363165 230697_at 170228679 170335841 UCHL5 70932 2904839 1268 0 0.007122593 62 8 chr1 −1 192987535 193028539 220083_x_at 192778234 192957607 NUDC 94796 500803 57244 0 0.007139932 100 100 chr1 1 27248217 27273353 210574_s_at 27343013 27420641 ZNF670 216 151321 71674 0 0.007142127 0 0 chr1 −1 247200086 247242057 223898_at 247242273 247262239 WFS1 3411 2476 1841 0 0.007150778 12 0 chr4 1 6271576 6304610 1555270_a_at 6225827 6268165 NFIA 40838 50567 1255 774 0.00715277 100 100 chr1 1 61547980 61928465 226806_s_at 61332157 61507142 TNNC2 2447 65790 42493 0 0.007199876 0 0 chr20 −1 44451853 44462384 205388_at 44453207 44459937 CWH43 563 0 80364 0 0.007205399 96 100 chr4 1 48988264 49064096 220724_at 48988827 49138512 KIAA1199 70807 341262 810 0 0.007214607 100 0 chr15 1 81071684 81244117 212942_s_at 80992262 81000877 LRP11 9320 53146 58236 0 0.007229319 100 100 chr6 −1 150139934 150185162 225060_at 150163935 150175842 UBE2T 152230 117730 126950 0 0.007229319 100 100 chr1 −1 202300785 202311108 223229_at 202122325 202158878 SHCBP1 3840 73038 263620 163 0.00723122 88 4 chr16 −1 46614466 46655538 219493_at 46659378 46690504 MMP1 0 1384100 329279 293384 0.007323802 100 38 chr11 −1 102660651 102668891 204475_at 102461598 102927599 SDCCAG8 6806 205980 12151 582 0.00733569 0 0 chr1 1 243419358 243663394 227785_at 243426164 243432981 CENPI 28109 2081 1024583 2149 0.007348151 8 0 chrX 1 100355426 100418670 207590_s_at 100322117 100327317 PTGDR 12721 0 1113 0 0.007362564 38 75 chr14 1 52734431 52743442 234165_at 52747152 52773244 E2F7 1762 116510 259553 0 0.007372299 71 0 chr12 −1 77415026 77459360 228033_at 77461122 77718302 CHCHD7 6521 23090 53987 0 0.007411413 8 4 chr8 1 57124357 57131174 218642_s_at 57075584 57117836 FSTL5 0 0 1921 1002275 0.007411413 0 0 chr4 −1 162305049 163085187 232010_at 161308668 164025969 SNRPA1 22184 16991 29468 0 0.007481179 100 100 chr15 −1 101821715 101835487 216977_x_at 101800931 101813303 ANXA10 0 40240 857281 225884 0.007571785 8 0 chr4 1 169013666 169108841 210143_at 168164267 169123358 CATSPERB 169343 0 156080 103789 0.00757793 17 0 chr14 −1 92047118 92198413 220293_at 92012720 92029070 SCRN1 65215 95938 105001 0 0.007586555 38 96 chr7 −1 29959719 30029414 201462_at 29846782 29964199 NOS2 1202 0 195863 6580 0.007649679 46 21 chr17 −1 26083792 26127525 210037_s_at 26128727 26142314 SPTLC1 140 692515 164591 0 0.007699666 25 0 chr9 −1 94841343 94877665 1554053_at 94877805 94903458 82812 157890 0 162117 0.007737899 4 0 chr1 1 183155488 183209534 207517_at 183238300 183365030 TTC26 134 319063 96385 0 0.007775656 0 0 chr7 1 138818524 138876732 219758_at 138818658 138824296 HPGD 29020 0 897 211 0.007836885 100 100 chr4 −1 175411328 175444049 203913_s_at 175473069 175750280 CXCL14 10624 0 0 0 0.00785922 100 100 chr5 −1 134906376 134914754 218002_s_at 134885256 134904130 FOSL1 28251 394572 12506 0 0.007861179 4 0 chr11 −1 65660060 65667997 204420_at 65696248 65712296 MTUS2 0 0 306572 203849 0.00787038 0 0 chr13 1 29598748 30077892 214961_at 29394960 30082468 SYT1 1827 331903 0 59372 0.007901212 4 0 chr12 1 79257773 79844059 203998_s_at 77719476 79255946 SPRR1B 0 0 229601 270339 0.007908228 0 0 chr1 1 153003678 153005376 205064_at 152590080 153227464 CELSR3 29283 285351 294 0 0.007913195 8 0 chr3 −1 48673902 48700348 40020_at 48665793 48671065 PLAC8 18960 35022 369255 4645 0.007920803 100 100 chr4 −1 84011201 84035955 219014_at 84054915 84091835 TTYH3 463 331890 8525 0 0.007931402 4 0 chr7 1 2671585 2704436 224674_at 2652027 2671122 PAIP1 150472 132937 43152 0 0.007964417 100 100 chr5 −1 43526369 43557181 209063_x_at 43707653 44801662 WASF1 5015 72104 177474 237 0.008018388 0 0 chr6 −1 110421022 110501204 204165_at 110305944 110496189 FIGNL1 15639 24459 227 0 0.008059769 96 58 chr7 −1 50511831 50518048 222843_at 50411178 50502409 CAB39L 40439 673735 94785 42387 0.008123848 21 0 chr13 −1 49882786 49975735 225914_s_at 49910626 49935296 TBX3 24750 0 2373 0 0.00818073 92 0 chr12 −1 115108059 115121969 225544_at 115146719 115165673 HOXA3 34357 0 4121 2874 0.008207064 75 100 chr7 −1 27145803 27159214 235521_at 26906410 27124857 PLAUR 22004 113659 28944 1249 0.008221225 62 79 chr19 −1 44152732 44174502 211924_s_at 44144524 44152498 THEM4 233 68907 463 0 0.008372633 4 0 chr1 −1 151846060 151882284 243492_at 151882517 151889814 DHRS11 22529 27559 49515 0 0.008390721 100 100 chr17 1 34948329 34957235 218756_s_at 34970858 34995823 GPR160 12606 88220 67957 68 0.008451173 100 100 chr3 1 169755527 169801918 223423_at 169715685 169742921 SLC11A2 119326 801726 145824 1660 0.008462409 100 100 chr12 −1 51379775 51422008 203123_s_at 51222303 51302682 MCM4 27413 243954 552986 0 0.008507646 96 88 chr8 1 48873494 48890068 222036_s_at 48900907 48917534 FCGRT 91398 67431 22007 912 0.008507809 100 100 chr19 1 50015620 50029588 218831_s_at 49868900 49924222 FAM89A 1723 17386 7712 0 0.00851459 0 0 chr1 −1 231154704 231175992 226448_at 231166967 231174269 VMO1 24107 136479 0 167 0.008538416 4 0 chr17 −1 4688581 4689731 235751_s_at 4649629 4665624 CHFR 9151 454256 0 0 0.008542648 79 100 chr12 −1 133416938 133464184 218803_at 133408647 133455033 CENPN 34230 107603 90470 32 0.008622413 8 0 chr16 1 81040103 81065090 222118_at 81074333 81080865 PAQR5 69804 178339 155373 0 0.008637134 96 100 chr15 1 69591286 69699986 242871_at 69513721 69521482 ATP5L 41972 47313 75356 158 0.008637134 100 100 chr11 1 118272104 118280559 208745_at 118154350 118230132 ZCCHC17 38485 137572 115437 0 0.008662099 0 0 chr1 1 31769842 31837783 223107_s_at 31714207 31731357 ITGA5 277 30684 0 0 0.008703242 0 0 chr12 −1 54789049 54813050 201389_at 54813327 54945812 CCNB1IP1 33109 61008 68385 80401 0.008707548 100 100 chr14 −1 20779529 20801169 217988_at 20193580 20768060 BMP7 5454 0 0 0 0.008717821 4 0 chr20 −1 55743804 55841684 209590_at 55847138 55925397 AMT 11020 124811 5525 6293 0.008718676 100 100 chr3 −1 49454212 49460186 204294_at 49471206 49481487 RASSF6 33 55128 323449 6 0.00874794 100 100 chr4 −1 74437267 74486265 229147_at 74486298 74535501 SPIRE1 21223 438132 9561 0 0.00875898 4 0 chr18 −1 12446512 12658133 1559517_a_at 12441323 12636910 COL17A1 0 5749 32184 35690 0.008769642 100 100 chr10 −1 105791044 105845760 204636_at 105844743 105868832 ATP8B1 79054 200036 289920 70018 0.00879718 100 100 chr18 −1 55313658 55399039 226302_at 55478093 55674977 CDKN1A 27016 274412 64539 0 0.00879718 100 100 chr6 1 36646435 36655116 202284_s_at 36673451 36686525 PRIM2 6588 129620 96796 95110 0.008843523 83 29 chr6 1 57182422 57398317 215708_s_at 57138323 57175834 WDR72 0 0 2906 3070 0.008858464 92 21 chr15 −1 53805938 54055075 227174_at 54052067 55473630 PLCB1 14935 160823 0 61 0.008858464 71 33 chr20 1 8112824 8865547 213222_at 8127759 8559260 FDPS 141476 135266 3386 0 0.008878079 100 100 chr1 1 155278643 155290456 201275_at 155113201 155137167 BCL2 51274 128340 616934 0 0.008898763 79 100 chr18 −1 60790579 60987361 203685_at 61038635 61057090 TMEM182 104499 29798 113058 0 0.008903431 12 0 chr2 1 103353367 103433875 1553301_a_at 103457866 105456231 NGFRAP1 3709 0 160573 54 0.00890749 100 100 chrX 1 102631268 102633005 217963_s_at 102634977 102811380 KIAA1524 36645 122701 285591 3618 0.008969512 58 0 chr3 −1 108268833 108304610 231855_at 108209044 108267965 CDKN1C 23286 173545 3082 0 0.009058443 0 0 chr11 −1 2904443 2906970 219534_x_at 2872158 2883684 TGIF2 10295 145304 31489 0 0.009072496 0 0 chr20 1 35201891 35222353 218724_s_at 35172560 35191596 NEIL3 1918 732017 516274 0 0.009072496 42 0 chr4 1 178230990 178284097 219502_at 177721702 178229072 C4BPA 0 0 51888 50764 0.009104341 29 4 chr1 1 207277607 207318317 205654_at 207260913 207425013 PIGX 11244 236375 75360 0 0.00910822 71 4 chr3 1 196439229 196462878 1552291_at 196371361 196427985 CBFA2T3 0 0 14059 9079 0.00912857 8 0 chr16 −1 88941266 89043373 208056_s_at 89008629 89156863 PLA2G16 82511 78484 16350 0 0.009172671 79 33 chr11 −1 63341946 63381909 209581_at 63274913 63299398 EPB41L3 7072 0 1 0 0.009186762 50 100 chr18 −1 5392383 5544241 211776_s_at 5301384 5537169 EIF2B3 255406 55132 173037 0 0.009186762 29 0 chr1 −1 45316450 45452282 218488_at 45148672 45196876 DGAT2 61730 7425 418080 0 0.009217032 92 0 chr11 1 75479778 75512579 226064_s_at 75388873 75418048 ZNF643 10028 110698 1567 643 0.009236976 0 0 chr1 1 40916716 40929390 207219_at 40897051 40906688 KCNMB4 5674 73672 1007196 0 0.009239329 4 0 chr12 1 70760062 70824978 222857_s_at 70765736 70916353 MSLN 0 52594 14376 14083 0.009240689 75 8 chr16 1 812594 818865 204885_s_at 795707 837324 MARCKS 8384 254767 483895 1194 0.009288164 100 100 chr6 1 114178541 114184648 225897_at 114154848 114170157 PRR15 40581 0 3694 98 0.009293264 100 100 chr7 1 29603427 29606911 226961_at 29644008 29680839 FAM127B 0 0 814642 0 0.009297598 4 4 chrX −1 134184962 134186205 217948_at 134185573 134232424 LPL 7052 0 0 560 0.009299221 50 0 chr8 1 19796284 19824769 203549_s_at 19803336 20054515 BRCA2 96 447610 224177 0 0.00933262 29 0 chr13 1 32889611 32973347 214727_at 32605926 32889515 NR3C2 7568 0 4869 0 0.00933262 100 100 chr4 −1 148999913 149365850 205259_at 149373418 149550514 SSX2IP 7856 291185 201941 0 0.00933262 8 0 chr1 −1 85109390 85156228 203019_x_at 85164084 85353693 HOMEZ 37722 74852 65659 0 0.00933262 0 0 chr14 −1 23742844 23755309 231868_at 23653907 23717587 TEAD2 3186 22475 21505 23 0.009338709 38 0 chr19 −1 49843857 49865714 238323_at 49868900 49924222 CHEK1 59968 69755 129286 198 0.009347576 96 12 chr11 1 125495036 125525640 205393_s_at 125555004 125751240 BUD31 98399 265801 14782 0 0.009352247 100 100 chr7 1 99006264 99017239 205690_s_at 98821222 98907865 SLFN13 6244 0 2263 2596 0.00937768 17 0 chr17 −1 33762115 33772699 1558217_at 33713350 33766455 STOX1 7417 422697 72450 0 0.009414804 4 0 chr10 1 70587298 70655188 1553202_at 70566017 70579881 SIAE 21625 41028 870 0 0.00948285 100 100 chr11 −1 124505694 124543763 224391_s_at 124565388 124588053 MET 2461 699681 950 0 0.009492357 71 0 chr7 1 116312446 116438440 213816_s_at 116166755 116309985 MS4A12 0 0 236324 22533 0.009502226 79 100 chr11 1 60260251 60274893 220834_at 59880038 60600316 DLAT 113522 379253 152426 39 0.009536442 100 100 chr11 1 111895538 111935114 213149_at 111755267 111782016 FAM40B 56026 281522 56894 0 0.009560713 0 0 chr7 1 129074287 129123472 1555292_at 128993853 129018261 FMR1 20272 0 588298 0 0.009585581 92 100 chrX 1 146993481 147031835 215245_x_at 146295424 146973209 APOLD1 19918 539869 29956 0 0.009618491 46 0 chr12 1 12878865 12944316 221031_s_at 12898783 12939687 29690 216356 25972 162 0.009660567 0 0 chr6 −1 30667584 30685666 203062_s_at 30715356 30743413 CYB5D1 63338 131788 132670 0 0.009681533 0 0 chr17 1 7761064 7765598 1552711_a_at 7664688 7697726 APOA2 4596 19959 34699 21161 0.009693688 0 0 chr1 −1 161192082 161193418 219465_at 161198014 161219016 SPATA6 12169 29569 303884 161 0.009695896 8 0 chr1 −1 48761044 48937845 220299_at 48950014 49242359 C3orf39 398 7566 560 0 0.009727032 0 0 chr3 −1 43120724 43147431 225689_at 43147829 43320434 WFS1 3411 2476 1841 0 0.009751162 54 0 chr4 1 6271576 6304610 202908_at 6225827 6268165 ALDH1B1 5946 7340 31117 0 0.009763351 100 58 chr9 1 38392661 38398658 209645_s_at 38398607 38421365 SLCO3A1 4664 7928 61741 0 0.009763351 17 0 chr15 1 92396925 92709133 227367_at 92090952 92392261 FCAR 0 0 212242 65087 0.009797727 0 0 chr19 1 55385736 55401838 207674_at 55372699 55550348 NPHP1 24 159907 90713 0 0.009808754 12 0 chr2 −1 110879888 110962619 238844_s_at 110962643 110969823 NAPEPLD 309 93086 618 0 0.009834565 100 100 chr7 −1 102740223 102789679 226041_at 102769130 102789370 FOLH1 15944 0 0 181 0.009852821 0 0 chr11 −1 49168190 49230222 205860_x_at 48849695 49214278 THBS2 0 266063 0 5091 0.009852821 4 0 chr6 −1 169615875 169654139 203083_at 169616680 169952489 HELLS 73972 84437 1367 0 0.00985699 92 4 chr10 1 96305574 96361856 223556_at 96379546 96939818 RP9 522 645526 344222 0 0.00989954 0 0 chr7 −1 33134409 33149002 227035_x_at 33149524 33168630 TREX2 6242 29238 46893 0 0.009901824 67 0 chrX −1 152710178 152736045 207891_s_at 152742287 152756534 41518 191660 281725 37766 0.009960756 4 0 chr8 −1 95444175 95449165 220549_at 95490683 95496265

TABLE 16 Partial listing of regions with cancer-specific differential methylation (C-DMRs) at a FDR of 5%. colon. colon. chr start end delta M tumor normal fdr state name annotation region distance island distToIsla 2325 chr10 5774977 5775480 0.884039577 1.262918606 0.420204198 0 Some methylation ASB13 NM_024701 upstream 26431 Far −7274 3576 chr11 117907224 117907958 1.001570264 1.129919936 0.236686302 0 Some methylation TMEM25 NM_032780 inside 3800 Shore 0 6904 chr11 65947037 65948698 −0.882029631 0.824501834 1.694138469 0 Less methylation NPAS4 NM_178864 inside 2054 Shore −1064 13834 chr13 113615559 113616275 −0.913827499 1.138092601 1.910209397 0 Less methylation FAM70B NM_182614 inside 35597 Shore 0 18878 chr15 58474576 58476390 −0.805171203 0.407560089 1.181506906 0 No methylation ANXA2 NM_001002857 inside 1086 Far 651 31523 chr19 5159373 5160095 −1.014437008 1.521337314 2.518715498 0 Less methylation PTPRS NM_130854 inside 131718 Far 1469 31686 chr19 5297115 5297780 −0.932920958 0.29967316 1.256908951 0 No methylation PTPRS NM_130854 upstream 5302 Far −5054 32005 chr19 55631525 55632172 −0.846213883 0.704148578 1.674940533 0 Less methylation MYBPC2 NM_004533 inside 29216 Shore −4036 32467 chr19 60702435 60703541 −0.930609844 1.30766243 2.173488599 0 Less methylation NAT14 NM_020378 upstream 11689 Shore 3082 33832 chr20 33650044 33650445 0.88180542 1.935235972 1.053430552 0 More methylation SPAG4 NM_003116 downstream 21933 Shore 1688 37372 chr21 37858818 37859555 −1.163675835 0.490611645 1.65428748 0 No methylation DYRK1A NM_001396 upstream 49271 Far −402 38130 chr2 147061940 147063253 −0.858337503 0.992346964 1.906435228 0 Less methylation ACVR2A NM_001616 downstream 1341608 Shore −91 40126 chr22 35335058 35336773 −1.037291011 1.139288 2.182025256 0 Less methylation CACNG2 NM_006078 inside 92075 Shore −44058 41538 chr22 48414225 48414719 −0.96407167 1.159071722 2.123143393 0 Less methylation C22orf34 NM_001039473 inside 22470 Far −1806 44705 chr3 193607217 193607552 −0.935728144 0.885876325 1.898131578 0 Less methylation FGF12 NM_021032 inside 1153 Far 960 45816 chr3 82629728 82630444 −0.837733539 0.977708408 1.768733642 0 Less methylation GBE1 NM_000158 upstream 736294 Shore 309227 47784 chr4 62618513 62619190 −0.87266859 1.84179962 2.691995246 0 Less methylation LPHN3 NM_015236 inside 1571 Far −552670 49706 chr5 1718578 1720081 −1.006675313 1.152316522 2.178490529 0 Less methylation MRPL36 NM_032479 downstream 132864 Shore 106 54115 chr6 52637426 52638797 −0.887556038 0.387977123 1.292585668 0 No methylation TMEM14A NM_014051 downstream 20544 Shore 0 56085 chr7 153219537 153220325 −1.02673515 0.690401085 1.588873129 0 Less methylation DPP6 NM_001039350 inside 1096601 Shore −2938 57345 chr7 27106893 27108170 0.882121475 1.490759927 0.681905484 0 More methylation HOXA2 NM_006735 inside 748 Far 1536 61903 chr8 819298 820365 −0.874467186 0.96711901 1.87443307 0 Less methylation ERICH1 NM_207332 upstream 148073 Far 1879 64837 chr9 94989150 94990319 0.845241759 1.311616403 0.49341257 0 Some methylation WNK2 NM_006648 inside 132354 Shore −1494 65721 chrX 135941512 135943110 0.904877352 0.842032974 −0.068886929 0 Some methylation GPR101 NM_054021 promoter 14 Shore 0 14300 chr13 24843229 24844191 0.835162395 1.564834811 0.706498375 2.95E−12 More methylation ATP8A2 NM_016529 downstream 649227 Shore 0 60198 chr8 144543158 144544935 −0.796122139 0.657035363 1.656096515 3.04E−12 Less methylation RHPN1 NM_052924 upstream 7196 Shore −9061 33157 chr20 15408602 15408931 −0.877118107 0.624232323 1.538178033 5.30E−12 Less methylation C20orf133 NM_001033087 inside 572907 Shore 1092905 30814 chr19 43436599 43438474 0.828947084 1.841118609 1.065766155 6.70E−12 More methylation PPP1R14A NM_033256 inside 537 Shore 4 57366 chr7 27121979 27122917 0.793013224 1.329883346 0.487838224 1.34E−11 Some methylation HOXA3 NM_030661 inside 2821 Far −28 980 chr10 129973472 129974329 −0.791044282 1.191324369 1.95202271 1.92E−11 Less methylation MKI67 NM_002417 upstream 158828 Far −19204 55445 chr7 129912736 129913242 −0.824647723 0.572058383 1.347853705 2.24E−11 Less methylation MEST NM_177524 downstream 20122 Shore 11 19785 chr15 90735153 90735977 −0.780988544 0.805516346 1.521399712 4.62E−11 Less methylation ST8SIA2 NM_006011 downstream 76982 Shore 1704 40200 chr22 36145002 36145832 0.778035539 1.115864323 0.401317933 5.64E−11 Some methylation LRRC62 NM_052906 upstream 43478 Shore 0 49841 chr5 175019374 175020506 −0.773226995 0.814882726 1.578348104 7.72E−11 Less methylation HRH2 NM_022304 downstream 23655 Far −1012 59441 chr8 118032313 118033443 −0.769581485 0.797225434 1.573042397 8.22E−11 Less methylation LOC441376 NM_001025357 upstream 7911 Shore −12173 57396 chr7 27151643 27153628 0.720370124 1.475288315 0.751826211 8.57E−11 More methylation HOXA6 NM_024014 inside 264 Shore 0 8775 chr12 108883476 108884015 −0.79920787 1.742699258 2.498324416 8.98E−11 Less methylation GIT2 NM_139201 inside 34467 Far 34165 57951 chr7 4865828 4866751 −0.752290368 0.579969952 1.276474622 1.80E−10 Less methylation PAPOLB NM_020144 inside 1399 Far 1111 19143 chr15 70198422 70199761 −0.756651884 0.328158957 1.123706438 2.30E−10 No methylation SENP8 NM_145204 inside 20595 Far −366 32707 chr19 63146186 63149953 −0.693139257 1.2067458 2.101579723 2.31E−10 Less methylation ZNF256 NM_005773 inside 935 Far 545 9574 chr12 128898887 128900474 −0.720321969 0.291118321 0.863809773 3.16E−10 No methylation TMEM132D NM_133448 inside 53691 Shore 5162 5439 chr1 14092469 14093393 0.743518354 1.950039432 1.157238839 3.74E−10 More methylation PRDM2 NM_012231 upstream 68308 Far −145 34856 chr20 56858718 56860946 0.682356929 1.097259392 0.353022441 3.76E−10 Some methylation GNAS NM_016592 inside 58697 Island 0 54056 chr6 50873235 50873811 −0.772772257 0.71134484 1.293278883 3.81E−10 Less methylation TFAP2B NM_003221 downstream 45822 Shore 21434 62237 chr9 101171244 101172098 −0.742206353 1.451503765 2.162847317 4.84E−10 Less methylation SEC61B NM_006808 upstream 138524 Far −72210 55753 chr7 145026589 145027407 −0.738007248 0.853276734 1.545617074 7.53E−10 Less methylation CNTNAP2 NM_014141 downstream 2721611 Shore 416556 7404 chr11 73980533 73981178 −0.784853788 0.605105525 1.389959312 8.52E−10 Less methylation POLD3 NM_006591 downstream 50234 Shore 0 49578 chr5 16236219 16237106 −0.727976294 0.319286099 1.034134495 1.00E−09 No methylation FBXL7 NM_012304 upstream 243320 Far −2799 63454 chr9 137437549 137438193 −0.745855742 0.943703974 1.666021652 1.27E−09 Less methylation KIAA0649 NM_014811 downstream 82366 Shore 6096 60504 chr8 17060922 17062917 −0.684418678 0.524740457 1.214365839 1.34E−09 Less methylation ZDHHC2 NM_016353 inside 61694 Far −1761 63300 chr9 136758751 136759638 −0.721949494 1.187281075 1.831695978 1.46E−09 Less methylation COL5A1 NM_000093 inside 116868 Shore 40696 28167 chr18 73809395 73809862 −0.761987843 0.712040225 1.397770327 1.78E−09 Less methylation GALR1 NM_001480 upstream 698315 Far 9620 43646 chr3 129687777 129688211 0.765371171 1.045816916 0.248273603 1.99E−09 Some methylation GATA2 NM_032638 inside 6506 Shore 0 44692 chr3 191521264 191521946 −0.736310316 0.305208673 0.941463033 2.29E−09 No methylation CLDN1 NM_021101 inside 962 Far 562 14770 chr13 42886712 42887185 −0.755363018 0.485004123 1.152369344 2.66E−09 No methylation PIG38 NM_017993 inside 252469 Shore 370673 57384 chr7 27147025 27148414 0.687423459 1.392236867 0.69627026 2.78E−09 More methylation HOXA5 NM_019102 overlaps 3′ 1397 Shore 724 42160 chr2 4028054 4028969 −0.716859847 1.030407359 1.739677942 2.80E−09 Less methylation ALLC NM_199232 upstream 299922 Island 0 26127 chr17 74692697 74693892 −0.705530207 0.763221549 1.574707214 2.93E−09 Less methylation LOC146713 NM_001025448 downstream 237673 Far −873 8908 chr12 112557312 112558104 −0.753141903 1.042028792 1.710085381 3.06E−09 Less methylation LHX5 NM_022363 upstream 163053 Far −43177 34318 chr20 44094989 44097868 −0.676720601 0.260559817 0.813306387 3.15E−09 No methylation SLC12A5 NM_020708 inside 24327 Far −634 58791 chr7 92075312 92075873 −0.755796746 0.73620026 1.585335161 3.60E−09 Less methylation CDK6 NM_001259 inside 225274 Shore −17503 57976 chr7 50103520 50103993 −0.743374995 0.807983185 1.493863455 5.51E−09 Less methylation ZPBP NM_007009 promoter 149 Far −53 38447 chr2 172826386 172826961 −0.729008517 0.432491545 1.192572807 5.75E−09 No methylation DLX2 NM_004405 upstream 150663 Shore −18042 59135 chr8 1032896 1034248 −0.687184842 0.539672279 1.258802261 5.85E−09 Less methylation ERICH1 NM_207332 upstream 361671 Far 1718 34832 chr20 56841054 56842229 −0.676159209 0.397024805 1.076612063 7.76E−09 No methylation GNAS NM_016592 downstream 77414 Shore 5761 57370 chr7 27129188 27131713 0.628259986 1.460162662 0.834558503 7.80E−09 More methylation HOXA3 NM_153631 inside 1450 Shore 0 22668 chr16 86201868 86205260 −0.678519462 0.923526175 1.762011152 9.80E−09 Less methylation JPH3 NM_020655 inside 83999 Shore 327 27359 chr18 32022373 32023451 −0.682417577 1.013390788 1.725157179 1.01E−08 Less methylation MOCOS NM_017947 inside 79230 Far −230 20997 chr16 31139986 31140921 −0.701244098 1.041352011 1.764370993 1.03E−08 Less methylation TRIM72 NM_001008274 inside 3089 Shore 2105 66376 chrX 23042002 23042577 −0.737872027 0.72397743 1.521827355 1.05E−08 Less methylation DDX53 NM_182699 upstream 111878 Shore 217628 10059 chr12 16648817 16649638 0.693702713 0.965838459 0.240165199 1.13E−08 Some methylation LMO3 NM_018640 inside 1059 Far −693016 4628 chr11 2190993 2192468 −0.654016557 0.728706953 1.344128093 1.36E−08 Less methylation TH NM_000360 upstream 41383 Shore −46172 52759 chr6 168586102 168588777 0.621864525 1.229549259 0.709159744 1.36E−08 More methylation SMOC2 NM_022138 inside 221818 Shore −153 46821 chr4 172202321 172202941 −0.710142653 1.176641595 1.899312607 1.39E−08 Less methylation GALNT17 NM_001034845 downstream 1996342 Shore 767368 33981 chr20 3603786 3604568 −0.692611023 0.436419597 1.130207665 1.43E−08 No methylation ADAM33 NM_025220 inside 6169 Shore −1013 55137 chr7 1182527 1183550 −0.701093724 0.584832729 1.240497677 1.53E−08 Less methylation ZFAND2A NM_182491 upstream 16204 Far −15857 41004 chr2 242632926 242634574 −0.699239495 1.216656053 1.917461412 2.62E−08 Less methylation FLJ33590 NM_173821 upstream 168280 Shore 1740 17867 chr14 95577239 95578925 −0.646974007 0.433930917 0.991416457 3.05E−08 No methylation C14orf132 NM_020215 inside 50960 Shore −1084 62117 chr8 966339 968282 −0.625531408 1.036720214 1.662365404 3.25E−08 Less methylation ERICH1 NM_207332 upstream 295114 Shore −581 65865 chrX 142544143 142544508 −0.728714637 0.713998945 1.304872981 3.62E−08 Less methylation SLITRK4 NM_173078 inside 6176 Far 4568 57988 chr7 50436454 50438081 −0.637817371 0.612478628 1.510098644 3.80E−08 Less methylation IKZF1 NM_006060 overlaps 5′ 0 Shore −560 15376 chr13 87123702 87125149 0.640539634 0.720765875 0.169112114 3.98E−08 Some methylation SLITRK5 NM_015567 inside 4719 Shore 0 12514 chr12 88272781 88274261 −0.65038077 0.929225424 1.579606194 4.42E−08 Less methylation DUSP6 NM_001946 upstream 2355 Far −506 13142 chr13 112142200 112143003 −0.678295439 0.658334617 1.327603281 4.68E−08 Less methylation C13orf28 NM_145248 upstream 5199 Far 11335 58570 chr7 80386676 80389252 −0.601910229 0.476007171 1.05329169 4.84E−08 No methylation SEMA3C NM_006379 promoter 74 Shore −14 58751 chr7 90064351 90065062 0.677011457 0.690804337 0.05018534 5.06E−08 Some methylation PFTK1 NM_012395 downstream 612777 Far −51 59080 chr8 100031456 100033208 0.618925139 0.940654534 0.235287751 5.12E−08 Some methylation OSR2 NM_053001 inside 291 Far −842 12935 chr13 110126686 110127336 0.682652476 1.946777838 1.27856897 5.44E−08 More methylation FLJ12118 NM_024537 inside 29127 Shore 1831 61933 chr8 846979 849372 −0.596646108 0.55360301 1.131506643 5.47E−08 Less methylation ERICH1 NM_207332 upstream 175754 Far −6574 3269 chr11 103540808 103541706 −0.672096716 0.914417143 1.675406973 5.56E−08 Less methylation PDGFD NM_025208 upstream 572 Shore −540 44954 chr3 28591265 28591843 0.687620751 0.820959578 0.117410558 6.39E−08 Some methylation ZCWPW2 NM_001040432 upstream 49632 Shore 0 62175 chr8 98356982 98358151 −0.641614569 1.081648716 1.732896661 6.46E−08 Less methylation TSPYL5 NM_033512 inside 1200 Shore 629 50428 chr5 3586182 3587073 −0.706076627 0.832023199 1.552694773 6.57E−08 Less methylation IRX1 NM_024337 downstream 67442 Far 1557 34521 chr20 4928754 4929383 0.695670621 0.737084605 0.05345522 6.64E−08 Some methylation SLC23A2 NM_005116 inside 761 Shore 111977 9576 chr12 128900526 128905070 −0.566798145 0.601192264 1.087718526 8.89E−08 Less methylation TMEM132D NM_133448 inside 49095 Far 566 51194 chr5 7900127 7901201 −0.656770027 0.625665717 1.352285824 9.34E−08 Less methylation FASTKD3 NM_024091 downstream 20913 Far 1744 30182 chr19 35406489 35408138 0.619251049 0.697131292 0.07706136 9.87E−08 Some methylation ZNF536 NM_014717 downstream 332666 Island 0 57697 chr7 3984090 3985861 −0.619295823 0.657262411 1.441495463 9.87E−08 Less methylation SDK1 NM_152744 inside 285898 Shore 134310 28407 chr18 75366596 75367142 −0.770077524 1.031079534 1.801157059 1.07E−07 Less methylation NFATC1 NM_172389 inside 23167 Shore 4639 48611 chr5 11954677 11955633 −0.645408794 1.247918641 1.825251349 1.12E−07 Less methylation CTNND2 NM_001332 inside 1476 Far 917 4640 chr11 2243719 2244678 −0.641643739 0.897753903 1.618595497 1.20E−07 Less methylation ASCL2 NM_005170 downstream 4079 Shore 2002 63374 chr9 137111474 137112189 −0.659852348 0.896213837 1.550180764 1.32E−07 Less methylation OLFM1 NM_006334 inside 17578 Far −3926 57568 chr7 32076356 32076691 0.709312665 0.683771808 0.032096544 1.58E−07 Some methylation PDE1C NM_005020 inside 824 Shore 0

TABLE 17 Regions with consistent cancer-specific differential methylation (C-DMRs) at a FDR of 5%. DeltaM is cancer minus normal. FDR is false discovery rate. Columns are chromo some, start, end, delta M, fdr, gene, relation to gene, distance to TSS, relation to CGI, distance to CGI chr start end deltaM fdr gene name relation TSS distance CGI distToCGI chr7 153219537 153220325 −1.02673515 1.31E−06 DPP6 inside 1096601 Far −2938 chr21 37858785 37859555 −1.084012454 1.64E−06 DYRK1A upstream 49238 Shore −369 chr11 117907224 117907958 1.001570264 3.28E−06 TMEM25 inside 3800 Shore 0 chr19 5159412 5160095 −1.022283546 6.28E−06 PTPRS inside 131718 Shore 1469 chr11 65947037 65948698 −0.882029631 6.38E−06 NPAS4 inside 2054 Shore −1064 chr22 35335058 35337265 −0.871428279 6.65E−06 CACNG2 inside 91583 Far −44058 chr19 60702504 60703541 −0.941226599 8.92E−06 NAT14 upstream 11758 Far 3082 chrX 135941512 135943110 0.904877352 9.30E−06 GPR101 promoter 14 Island 0 chr6 52637426 52638797 −0.887556038 1.30E−05 TMEM14A downstream 20544 Shore 0 chr7 27106893 27108203 0.870705583 1.56E−05 HOXA2 inside 715 Shore 1503 chr5 1718233 1720117 −0.859031092 2.05E−05 MRPL36 downstream 132828 Shore 70 chr19 5297115 5297780 −0.932920958 2.26E−05 PTPRS upstream 5302 Far −5054 chr2 147061970 147063253 −0.860149055 2.29E−05 ACVR2A downstream 1341608 Shore −121 chr8 819298 820365 −0.874467186 2.43E−05 ERICH1 upstream 148073 Shore 1879 chr22 48414225 48414719 −0.96407167 2.49E−05 C22orf34 inside 22470 Shore −1806 chr13 113615559 113616275 −0.913827499 2.70E−05 FAM70B inside 35597 cover 0 chr15 58474612 58476390 −0.81855457 3.99E−05 ANXA2 inside 1086 Shore 651 chr7 3984567 3985861 −0.840761885 6.63E−05 SDK1 inside 285898 Far 134310 chr20 33650044 33650409 0.94650255 6.95E−05 SPAG4 downstream 21969 Shore 1724 chr13 24843229 24844069 0.886018997 7.38E−05 ATP8A2 downstream 649349 Shore 0 chr4 62618513 62619190 −0.87266859 7.61E−05 LPHN3 inside 1571 Far −552670 chr3 193607217 193607552 −0.935728144 0.000111597 FGF12 inside 1153 Shore 960 chr10 5774977 5775480 0.884039577 0.000120662 ASB13 upstream 26431 Far −7274 chr3 82629728 82630444 −0.837733539 0.000141351 GBE1 upstream 736294 Far 309227 chr15 70198455 70199761 −0.825003332 0.000148319 SENP8 inside 20595 Shore −399 chr8 144543158 144544971 −0.770400642 0.000172289 RHPN1 upstream 7196 Far −9061 chr19 63146186 63149398 −0.700896124 0.000209459 ZNF256 inside 1490 Shore 1100 chr7 27121979 27122917 0.793013224 0.000214766 HOXA3 inside 2821 Shore −28 chr10 129973472 129974329 −0.791044282 0.000243982 MKI67 upstream 158828 Far −19204 chr5 175019374 175020470 −0.786575281 0.000320566 HRH2 downstream 23691 Shore −1012 chr15 90735153 90736013 −0.774643272 0.000336501 ST8SIA2 downstream 76946 Shore 1668 chr20 15408602 15408931 −0.877118107 0.00036397 C20orf133 inside 572907 Far 1092905 chr12 128898887 128900474 −0.720321969 0.000387656 TMEM132D inside 53691 Far 5162 chr20 56858718 56860982 0.659681384 0.000397048 GNAS inside 58661 cover 0 chr8 118032349 118033443 −0.770523086 0.000399429 LOC441376 upstream 7947 Far −12209 chr19 55631492 55632172 −0.789979406 0.000409085 MYBPC2 inside 29216 Far −4003 chr7 27151538 27154015 0.661580605 0.000409085 HOXA6 covers 0 Shore 0 chr22 36144969 36145868 0.759848671 0.000411532 LRRC62 upstream 43445 Shore 0 chr20 16499527 16500276 −0.775760202 0.000435467 C20orf23 inside 1801 Shore 1560 chr7 4865828 4866751 −0.752290368 0.00043806 PAPOLB inside 1399 Shore 1111 chr8 17060922 17062917 −0.684418678 0.000513695 ZDHHC2 inside 61694 Shore −1761 chr12 108883476 108884015 −0.79920787 0.000559116 GIT2 inside 34467 Far 34165 chr1 14092469 14093393 0.743518354 0.000560746 PRDM2 upstream 68308 Shore −145 chr9 101171277 101172098 −0.751851067 0.000568963 SEC61B upstream 138557 Far −72243 chr7 27129188 27131713 0.628259986 0.00063513 HOXA3 inside 1450 cover 0 chr9 94987821 94990808 0.598842709 0.000698251 WNK2 inside 131865 Shore −165 chr7 145026589 145027407 −0.738007248 0.00073506 CNTNAP2 downstream 2721611 Far 416556 chr5 16236219 16237106 −0.727976294 0.000747719 FBXL7 upstream 243320 Far −2799 chr6 168586102 168588777 0.621864525 0.000780248 SMOC2 inside 221818 Shore −153 chr7 27147025 27148381 0.688088459 0.000795867 HOXA5 overlaps 3′ 1430 Shore 757 chr6 50873235 50873811 −0.772772257 0.000800382 TFAP2B downstream 45822 Far 21434 chr9 136758751 136759638 −0.721949494 0.000834999 COL5A1 inside 116868 Far 40696 chr17 74692733 74693892 −0.716568667 0.000851618 LOC146713 downstream 237673 Shore −909 chr20 44094989 44097479 −0.683544424 0.000863673 SLC12A5 inside 24716 Shore −634 chr12 128900559 128905004 −0.581538135 0.000893245 TMEM132D inside 49161 Shore 632 chr9 137437549 137438193 −0.745855742 0.001032389 KIAA0649 downstream 82366 Far 6096 chr8 1032932 1034329 −0.687184842 0.001090973 ERICH1 upstream 361707 Shore 1637 chr20 56841054 56842229 −0.676159209 0.001106085 GNAS downstream 77414 Far 5761 chr11 2190993 2192468 −0.654016557 0.001130661 TH upstream 41383 Far −46172 chr7 80386676 80389252 −0.601910229 0.001187784 SEMA3C promoter 74 Shore −14 chr8 846979 849372 −0.596646108 0.001191034 ERICH1 upstream 175754 Far −6574 chr3 191521264 191521946 −0.736310316 0.001220642 CLDN1 inside 962 Shore 562 chr3 193338227 193339771 −0.673047389 0.001237379 FGF12 downstream 268934 Far 268741 chr16 86201868 86205260 −0.678519462 0.00127148 JPH3 inside 83999 Shore 327 chr22 48392638 48393144 −0.760715735 0.001285358 C22orf34 downstream 44045 Shore 1818 chr8 966339 968246 −0.626496123 0.001295856 ERICH1 upstream 295114 Shore −581 chr11 73980533 73981178 −0.784853788 0.001331416 POLD3 downstream 50234 Shore 0 chr18 32022373 32023451 −0.682417577 0.001353174 MOCOS inside 79230 Shore −230 chr18 73809395 73809862 −0.761987843 0.001443472 GALR1 upstream 698315 Far 9620 chr13 113548528 113549312 0.709469821 0.001455135 GAS6 inside 41083 Shore −393 chr3 129687744 129688211 0.759314875 0.001514741 GATA2 inside 6506 Shore 0 chr14 95577239 95578964 −0.645499663 0.001518792 C14orf132 inside 50921 Shore −1084 chr7 92075312 92075740 −0.777130862 0.001522853 CDK6 inside 225407 Far −17503 chr12 16648850 16649638 0.700736708 0.001551557 LMO3 inside 1059 Far −693049 chr19 43436533 43438474 0.714930008 0.001597653 PPP1R14A inside 537 Shore 4 chr7 50436490 50438081 −0.639172776 0.001610437 IKZF1 overlaps 5′ 0 Shore −596 chr13 42886712 42887185 −0.755363018 0.001619012 PIG38 inside 252469 Far 370673 chr8 100031420 100033208 0.611013818 0.001627628 OSR2 inside 291 Shore −806 chr16 31139986 31140921 −0.701244098 0.001675759 TRIM72 inside 3089 Far 2105 chr13 87123702 87125116 0.642126998 0.001693577 SLITRK5 inside 4752 cover 0 chr2 172826386 172826961 −0.729008517 0.001729729 DLX2 upstream 150663 Far −18042 chr12 88272781 88274261 −0.65038077 0.001936245 DUSP6 promoter 2355 Shore −506 chr7 50103520 50103993 −0.743374995 0.001982182 ZPBP promoter 149 Shore −53 chr7 1182527 1183550 −0.701093724 0.002018587 ZFAND2A upstream 16204 Far −15857 chrX 23042002 23042541 −0.759184452 0.002060928 DDX53 upstream 111878 Far 217664 chr8 98356982 98358151 −0.641614569 0.00212045 TSPYL5 inside 1200 Shore 629 chr11 132451645 132454794 −0.551863416 0.002125937 OPCML inside 452818 Far 2108 chr4 172202321 172202941 −0.710142653 0.002125937 GALNT17 downstream 1996342 Far 767368 chr11 133791126 133793856 −0.564608575 0.002244148 B3GAT1 upstream 4105 Far −2997 chr7 129912706 129913314 −0.698922372 0.002556137 MEST overlaps 3′ 20050 Shore 0 chr12 38783104 38784488 0.607732473 0.002601858 SLC2A13 inside 1439 Shore 741 chr13 112142200 112143003 −0.678295439 0.00268194 C13orf28 upstream 5199 Far 11335 chr7 90064351 90065026 0.683927774 0.00268194 PFTK1 downstream 612813 Shore −51 chr11 103540808 103541706 −0.672096716 0.002722801 PDGFD promoter 572 Shore −540 chr21 42057698 42059424 −0.588799731 0.002743438 RIPK4 inside 893 Shore 0 chr2 4028568 4028969 −0.739275995 0.002855883 ALLC upstream 300436 Island 0 chr11 2243752 2244711 −0.641643739 0.002863045 ASCL2 downstream 4046 Shore 1969 chr5 11954677 11955633 −0.645408794 0.002877417 CTNND2 inside 1476 Shore 917 chr5 7900127 7901165 −0.662624905 0.002920922 FASTKD3 downstream 20949 Shore 1780 chr13 109229281 109231903 −0.549669563 0.003032257 IRS2 inside 5011 Shore 564 chr13 110126656 110127336 0.674417006 0.003124028 FLJ12118 inside 29127 Shore 1831 chr20 48778557 48780262 −0.595456871 0.00331501 PARD6B downstream 23421 Shore 510 chr14 100997052 100997806 −0.669615597 0.003372632 DIO3 downstream 101733 Shore −1304 chr3 28591265 28591843 0.687620751 0.003405956 ZCWPW2 upstream 49632 Shore 0 chr11 133445524 133446466 −0.659812073 0.003603295 JAM3 inside 80392 Shore −633 chr5 132392 134453 −0.575968981 0.003647512 KIAA1909 downstream 108624 Shore 1975 chrX 142544143 142544478 −0.743808544 0.003755595 SLITRK4 inside 6206 Far 4598 chr20 4928754 4929383 0.695670621 0.003773881 SLC23A2 inside 761 Far 111977 chr12 112557273 112558104 −0.692536013 0.00396112 LHX5 upstream 163014 Far −43138 chr16 85092993 85096638 0.4875436 0.003989902 FOXF1 downstream 8931 Shore 0 chr10 1437553 1439129 −0.58556974 0.00404802 ADARB2 inside 330540 Far −7539 chr2 242632887 242634574 −0.663580398 0.004057778 FLJ33590 upstream 168241 Shore 1740 chr2 4028054 4028513 −0.727374572 0.004067558 ALLC upstream 299922 Shore 11 chr19 35406489 35407329 0.646090813 0.004106883 ZNF536 downstream 333475 Shore 60 chr7 42233455 42234204 0.645603687 0.004136596 GLI3 upstream 4036 Shore 0 chr3 174341049 174341237 −0.801112836 0.00415651 SPATA16 inside 457 Far 254724 chr5 3586182 3587073 −0.706076627 0.00415651 IRX1 downstream 67442 Shore 1557 chr8 22469866 22470840 −0.625728011 0.004206665 SORBS3 inside 18110 Far −4286 chr6 10501022 10502013 0.65421633 0.004288023 TFAP2A downstream 18579 Shore −1938 chr11 31966319 31967492 −0.637486731 0.004339572 RCN1 downstream 116160 Shore −699 chr1 206062462 206063805 0.576184672 0.004476158 LOC148696 overlaps 5′ 0 Far 44680 chr22 47267034 47267870 −0.630643807 0.004476158 FAM19A5 downstream 265877 Shore −1327 chr6 80711271 80712497 −0.594390766 0.004508209 ELOVL4 inside 1443 Shore 966 chr22 47455137 47456387 −0.584007269 0.004551258 FAM19A5 inside 77360 Far −4801 chr11 134186796 134187368 −0.666896255 0.004693669 B3GAT1 upstream 399775 Far −48599 chr19 13474169 13475470 −0.622911411 0.004693669 CACNA1A inside 2846 Far 2282 chr16 25608094 25609031 −0.617716356 0.004749475 HS3ST4 downstream 447477 Shore 1425 chr8 117611158 117611838 −0.647479337 0.004749475 EIF3S3 downstream 225404 Far 225273 chr20 3603573 3604604 −0.598667161 0.004966877 ADAM33 inside 6133 Shore −800 chr20 59905352 59906092 −0.676814042 0.005037317 CDH4 inside 39601 Shore −1622 chr14 52326048 52327382 −0.59636953 0.005144616 GNPNAT1 inside 750 Shore 32 chr22 46984389 46985561 −0.585617065 0.005144616 LOC388915 upstream 66632 Shore −218 chr7 152249022 152250754 −0.636478846 0.00515666 ACTR3B upstream 65627 Far 2095 chr7 27108458 27111260 0.508492851 0.00515666 HOXA2 overlaps 5′ 0 cover 0 chr5 158465126 158466712 0.54868809 0.00532789 EBF1 upstream 5780 cover 0 chr7 149667109 149668386 0.570024092 0.005365221 RARRES2 inside 1252 Shore 6 chr10 3499370 3500060 −0.644793235 0.00540278 PITRM1 upstream 294368 Far −8794 chr11 31780765 31782111 0.582076146 0.005427947 PAX6 inside 7322 Shore 208 chr7 139121471 139122253 0.621563749 0.005529639 TBXAS1 downstream 244217 Shore 1622 chr17 14831980 14832519 −0.662742648 0.00555532 FLJ45831 upstream 207736 Far 272136 chr3 148446946 148448043 −0.61085168 0.005632988 ZIC4 downstream 159053 Far 111759 chr18 11140361 11141025 −0.641611395 0.005672176 FAM38B upstream 452548 Shore −425 chr19 4505154 4505834 −0.635384318 0.005698433 SEMA6B inside 3668 Shore 1102 chr4 81341228 81342411 0.593057633 0.005724795 PRDM8 inside 2092 Shore 121 chr13 100427954 100428562 −0.659465205 0.005831309 VGCNL1 downstream 438251 Far −302230 chr1 221053963 221054618 −0.658163166 0.005953193 FLJ43505 upstream 63194 Shore 249 chr9 97304533 97306772 0.538529057 0.005980578 PTCH1 inside 3879 Shore 1524 chr10 134597978 134600218 −0.585261073 0.006063388 C10orf93 inside 5835 Far 5435 chr10 24025367 24026498 −0.60528892 0.006119146 C10orf67 upstream 351590 Shore −383 chr19 50669649 50670313 0.642613368 0.006119146 FOSB overlaps 5′ 0 Shore −1547 chr18 491107 491721 0.648047368 0.006231999 COLEC12 promoter 423 Shore −385 chr17 41333049 41334735 −0.548189858 0.006260492 MAPT inside 126808 Far −2213 chr12 52430235 52431320 0.598152778 0.006361111 CALCOCO1 upstream 22750 Island 0 chr13 67580738 67581346 −0.639592071 0.006404661 PCDH9 upstream 878275 Far 875559 chr5 134553843 134554689 0.606657045 0.006419235 H2AFY downstream 208137 Shore 137 chr12 122813965 122816002 −0.550995205 0.006522058 ATP6V0A2 upstream 3575 Shore −758 chr20 24399131 24400197 0.576626292 0.006522058 C20orf39 inside 194969 Island 0 chr2 100303439 100304155 0.619440354 0.006641312 LONRF2 upstream 11041 Shore 56 chr13 21140646 21141533 0.594077102 0.006747202 FGF9 downstream 32650 Shore 0 chr8 132984463 132985363 −0.623396903 0.006793028 KIAA0143 downstream 109587 Shore 141 chr11 1861791 1862726 −0.59253943 0.006901003 LSP1 inside 7341 Shore −1881 chr10 101273278 101274941 0.562231173 0.006916548 NKX2-3 downstream 11326 Shore −348 chr13 113850844 113851732 0.592061228 0.006947729 RASA3 inside 64464 Far 2436 chr7 32076356 32076652 0.715435355 0.006994728 PDE1C inside 863 Shore 0 chr11 45645190 45645996 −0.605303898 0.007010455 CHST1 promoter 1443 Shore −1119 chr19 16876450 16876750 −0.746371667 0.007010455 CPAMD8 inside 121718 Far −6593 chr8 53636408 53637226 −0.600422547 0.007026213 UNQ9433 inside 3338 Far 2871 chr15 24571127 24572559 −0.554446179 0.00705782 GABRB3 promoter 1108 Shore −1091 chr6 133605067 133606789 0.529371985 0.00708955 EYA4 inside 287568 Shore 0 chr12 88266873 88268978 −0.496208684 0.0072177 DUSP6 inside 1448 Shore 321 chr17 782607 784014 −0.562507428 0.007233859 NXN inside 45745 Far 12943 chr19 36535076 36535822 0.607202133 0.007347841 TSHZ3 upstream 73062 Shore 0 chr13 20184925 20186542 −0.533916441 0.007413666 IL17D inside 8693 Far 7069 chr17 22902924 22903499 −0.634066178 0.007631109 KSR1 inside 71344 Far 53125 chr1 32992405 32992989 0.632485647 0.00780208 KIAA1522 inside 20168 Shore 0 chr15 32835765 32836849 −0.563189738 0.007923707 CX36 promoter 1785 Shore −993 chr12 130718351 130718755 −0.681706414 0.008011574 SFRS8 downstream 131479 Far −5588 chr13 36392772 36394298 0.523296289 0.008011574 ALG5 downstream 77178 Shore −20 chr20 61186047 61186916 −0.586579264 0.008011574 BHLHB4 upstream 77261 Shore 1296 chr11 19323912 19324590 0.644908853 0.008029248 E2F8 upstream 104830 inside 0 chr12 111302662 111303588 0.576207223 0.008207826 RPL6 downstream 28237 Island 0 chr15 97011564 97012941 0.531506065 0.008280203 IGF1R inside 306092 Shore 0 chr16 49141667 49142498 −0.597924762 0.008371442 NKD1 inside 83643 Shore −701 chr14 57669356 57669957 −0.633107389 0.008537837 C14orf37 inside 18642 Far 18087 chr8 144372893 144373912 −0.591419915 0.008556499 LOC338328 promoter 2476 Far 9171 chr9 124022303 124023189 0.590922099 0.008612692 LHX6 inside 7615 Shore 0 chr19 3240846 3241458 −0.618423464 0.008669201 BRUNOL5 inside 6612 Far 2809 chr16 4101996 4102769 0.59406133 0.008840627 ADCY9 inside 3417 Far 2040 chr12 4889938 4890628 0.610450142 0.008898408 KCNA1 close to 3′ 1662 inside 0 chr3 151719593 151721472 −0.528810826 0.00895651 SERP1 downstream 25645 Far 24824 chr19 41058856 41059386 −0.636595945 0.009034481 APLP1 inside 3151 Shore −1192 chr7 71437052 71438143 −0.553874961 0.009034481 CALN1 inside 1752 Shore 550 chr9 37023001 37023958 0.572428385 0.009192158 PAX5 inside 517 Shore 177 chr20 33336228 33337040 −0.586120135 0.009212032 FAM83C overlaps 3′ 6598 Shore −75 chr7 5360426 5361424 0.575877608 0.009311946 SLC29A4 upstream 50199 Shore 974 chr18 75366596 75367142 −0.770077524 0.009352169 NFATC1 inside 23167 Far 4639 chr6 7413675 7414250 −0.619224954 0.00939254 RIOK1 upstream 50409 Far 72267 chr11 64244495 64245421 −0.57059158 0.009433058 NRXN2 inside 1814 Shore 1648 chr16 7291114 7292175 −0.557798462 0.009494114 A2BP1 inside 408671 Far 2159 chr8 3257254 3257862 −0.611993878 0.009494114 CSMD1 inside 1581873 Far −389899 chr5 88221043 88221995 0.573950547 0.009555505 MEF2C upstream 6264 Island 0 chr13 99440030 99441015 0.573722467 0.009596619 ZIC2 upstream 3012 Shore 0 chr10 102811316 102812341 −0.552736003 0.009658572 KAZALD1 overlaps 3′ 2996 inside 0 chr17 71291527 71292204 −0.596863212 0.009888639 H3F3B upstream 4073 Shore 237 chr10 112248574 112249464 0.566330793 0.00999474 DUSP5 inside 11825 Shore 0

This application claims priority under 35 USC § 119(e) to U.S. Provisional Application Ser. No. 61/518,892, the entire content of which is incorporated by reference.

Although the invention has been described with reference to the above example, it will be understood that modifications and variations are encompassed within the spirit and scope of the invention. Accordingly, the invention is limited only by the following claims. 

What is claimed is:
 1. A method comprising: a) identifying an anti-profile in a sample from a subject comprising: i) determining the methylation status of a plurality of differentially methylated regions of genomic nucleic acid sequences from a non-cancerous biological sample and corresponding plurality of differentially methylated regions of genomic nucleic acid sequences in a test sample from the subject, wherein determining methylation status comprises detecting methylated and unmethylated nucleic acids in the differentially methylated regions, and utilizing an algorithm configured to quantile normalize raw intensity data from methylated and unmethylated nucleic acids and calculate methylation status as a ratio of methylated nucleic acid intensity over a sum of methylated and unmethylated nucleic acid intensity; and ii) performing statistical analysis to determine a methylation variance score for the non-cancerous sample and a methylation variance score for the test sample, and detecting increased stochastic variation in the methylation status of the test sample as compared to the non-cancerous sample, wherein at least 25 nucleic acids are analyzed; b) detecting expression of MMP3, MMP7, MMP10, or a combination thereof, in the sample; c) diagnosing the subject as having or at risk of having cancer, wherein the sample from the subject has increased stochastic variation in methylation status as compared to the non-cancerous sample; and d) administering a chemotherapeutic to the subject.
 2. The method of claim 1, wherein the plurality of differentially methylated regions of genomic nucleic acid sequences are small differentially methylated regions (sDMRs) as set forth in Table
 7. 3. The method of claim 2 comprising detecting, in a plurality of the sDMRs from the test sample, a loss of methylation boundary wherein the loss comprises an increase of methylation in a CpG island of the sDMR and a decrease of methylation in a nucleic acid sequence up to about 2 kb in distance from the CpG island as compared to methylation of a corresponding region in the non-cancerous biological sample.
 4. The method of claim 2 comprising detecting, in a plurality of the sDMRs from the test sample, a shift of methylation boundary comprising a similar level of methylation as compared to that of a corresponding region in the non-cancerous biological sample.
 5. The method of claim 2 comprising detecting, in a plurality of the sDMRs from the test sample, an increased level of methylation as compared to that of a corresponding region in the non-cancerous biological sample.
 6. The method of claim 1, wherein determining a methylation variance score comprises performing principal component analysis, a statistical F-test, or combination thereof.
 7. The method of claim 1, wherein the plurality of differentially methylated regions of genomic nucleic acid sequences are located outside of a promoter region of a gene and/or outside of a CpG island.
 8. The method of claim 1, wherein the method further comprises detecting a shift or loss of methylation boundary in one or more of the plurality of differentially methylated regions of genomic nucleic acid sequences from the test sample as compared to that of the corresponding plurality of differentially methylated regions of genomic nucleic acid sequences in the non-cancerous biological sample.
 9. The method of claim 1, wherein the cancer is selected from the group consisting of colorectal cancer, esophageal cancer, stomach cancer, leukemia/lymphoma, lung cancer, prostate cancer, uterine cancer, breast cancer, skin cancer, endocrine cancer, urinary cancer, liver cancer, thyroid cancer, kidney cancer, pancreas cancer, other gastrointestinal cancer, ovarian cancer, cervical cancer, head cancer, neck cancer, and adenomas.
 10. The method of claim 1, further comprising detecting expression of one or more additional genes selected from the group consisting of genes as set forth in FIG. 16A, FIG. 16B, Table 14 and Table
 15. 